[Freesurfer] Functional data analysis in qdec
Dear FS experts, I'm wondering whether is possible to perform vertex analyses on pet data using qdec, I'm running FS v5.3.0 under ubuntu 12.04. I have all my functional data converted to surfaces. Qdec 1.5 says that the functional design is not yet implemented. So, I'm wondering is there is a way to get my pet data into qdec? I have tried in every single subject: mris_preproc --s subj001 --hemi ?h --meas subjPetSurf.mgh --target myAVGsubj --out ?h.thickness.myAVGsubj.mgh And then just smooth the resulting surface, so the qdec might use my functional data as if it were the thickness. But I'm not sure if it is a good solution or I'm doing something wrong, because the results look so different from those on the command line group analyses. Any guidance here will be so appreciated! Many thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Help on DTI pre-processing
Dear all,I have a question regarding the pre-prossesing steps of DTI data.I have 5 different datasets, each with different acquisition parameters, including the number of directions (16, 32 and 64), the b-value (1000, 1300 and 1500) and the magnetic field (1.5 and 3T). Do you think that a single pre-processing procedure can be applied to all of them? or it will vary depending on the acquisition parameters?A second question would be, if the pre-processing steps of FS include some distortion correction using a high-resolution image? If so, could it be replaced by the T2 or a b0?Can you point me to the correct literature of this?Many thanks in advanced for your time and help,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DWI questions
Dear Freesurfer and DTI experts,I will start some analyses with DWI data, but I have some doubts about it:1) I have data with 5 different acquisition protocols, so, I'm not sure if the standard pre-processing protocol (like eddy-current compensations the reorientation of the vectors and the intra-subject registration) can be applied to all images equally or if I do need to set any specific parameters for each acquisition protocol?2) Does your method have any tool to check that the vectors are good, before or after fitting the tensors?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] MNI CONVERSION PROBLEM
I have tried several thing like opening on MriCroN and tkregister as:
tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg
/root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat
- Mensaje original -
De: Douglas N Greve gr...@nmr.mgh.harvard.edu
Fecha: Jueves, 27 de Marzo de 2014, 5:54 pm
Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
A: freesurfer@nmr.mgh.harvard.edu
The first one should be correct. How are you visualizing it?
What is the
command line?
On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
I have used both for the output of mni152reg:
mri_vol2vol --mov
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
targ
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--inv --o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz
and
mri_vol2vol --targ
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
mov
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz
I also have tried these two commands with the output matrix of
bbregister s001_register.dat
- Mensaje original -
De: Douglas Greve gr...@nmr.mgh.harvard.edu
Fecha: Jueves, 27 de Marzo de 2014, 4:11 am
Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
A: freesurfer@nmr.mgh.harvard.edu
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some
volumetric
labels of my subjects extracted with mris_extract_label in FS
v.5.1
but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them
give me
an example to check at the registrations using tktegister2,
when I
use it everything seems to be OK, but when I do apply with
mri_vol2vol any of the matrices to the volumetric masks, they
appear
to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced,
Gabriel
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font size=3--br /PhD.
student Gabriel
González-Escamillabr /Laboratory of Functional
Neurosciencebr
/Department of Physiology, Anatomy, and Cell Biologybr
/University
Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 -
Sevillebr
/- Spain -br /br /Email: ggon...@upo.esbr
/http://www.upo.es/neuroaging/es//font
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
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font size=3--br /PhD. student Gabriel
González-Escamillabr /Laboratory of Functional Neurosciencebr /Department
of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr
/Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email:
ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font
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[Freesurfer] MNI CONVERSION PROBLEM
Dear FS experts, I've been dealing with the conversion to MNI152 of some volumetric labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed. I've tried bbregister and mni152reg commands, both of them give me an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it. Any help will be really appreciated. Many thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] autorecon2 error
Dear Freesurfer experts,I'm using version 5.1 to segment some subjects, but I have one that is causing some troubles when executing the autorecon2 after some manual cleaning of non-brain tissue and some control points added, I always get the following error: ERROR: _FindFacePath: could not find path! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj2_01_yr3_PEPA exited with ERRORS at Wed Feb 5 02:41:04 CET 2014 I have tried to open the surfaces in tksurfer, the lh.orig looks real weird, also if I try to open both surfaces (lh.white and lh.orig) in tkmedit it outputs the next error: tkmedit subj2_01_yr3_PEPA brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white Reading 640 control points... Converting main surface: 100% done. Converting main surface: 100% done. mrisReadTriangleFile(/root/trabajo/freesurfer/subjects/subj2_01_yr3_PEPA/surf/lh.orig): surface doesn't match /root/trabajo/freesurfer/subjects/subj2_01_yr3_PEPA/surf/lh.white No such file or directory mrisReadTriangleFile failed. No such file or directory I have checked at the subj2_01_yr3_PEPA/surf folder and both surfaces exist. So, I don't have a clue on how to solve this.Does anyone has an idea how to fix this problem?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] glmfit error on v5.1
Dear Freesurfer experts,Sorry for the inconvenience but I posted this message last week, but I did not receive any answer. I really need to keep going on with my analyses.I have runned the following command line:mri_glmfit --surf PLI_MCI_sample7_avg lh --C /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/which is always prompts the following error:ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07Possible problem with experimental designI'm sending attached the fsgd.txt and contras.mat files used in case you need themDoes anyone knows what's wrong with my design?Many thanks in advanced,Gabriel. contrast_withinE4_neg.mat Description: Binary data GroupDescriptorFile 1 Title PVEc-PET_with_MRI in sig_clusters of MC_3000 Class E4female Class E4male Class noE4female Class noE4male variables zAge zAPOB zlh.cortex_AVGthickness Input mci_01_year1 noE4male -0.025380 -0.495746 -0.569553 Input mci_02_year1 noE4male 0.416237 -0.163064 -1.388804 Input mci_04_year1 noE4female -0.466997 -1.018533 1.324541 Input mci_10_year1 noE4male -0.319792 -1.351215 0.286936 Input mci_11_year1 noE4female 0.563442 -0.400694 -0.384206 Input mci_14_year1 noE4male -0.466997 -0.281879 0.611082 Input mci_15_year1 noE4female 1.152265 -0.567035 0.446893 Input mci_16_year1 noE4male 0.857854 0.549827 -1.563149 Input mci_20_year1 noE4male -0.614203 -1.066059 -0.254717 Input mci_23_year1 noE4male 1.299471 -0.780902 -0.043134 Input mci_25_year1 noE4male -0.761409 -0.899718 0.469744 Input mci_33_year1 noE4male -0.908614 0.858747 0.584846 Input mci_36_year1 noE4male -0.025380 2.260766 -0.997798 Input mci_38_year1 noE4male -2.822288 2.759790 1.354163 Input mci_39_year1 noE4male -1.350231 2.569685 0.621238 Input mci_06_year1 E4female -0.172586 -0.234353 -0.633028 Input mci_07_year1 E4male -1.350231 -0.139301 -0.126075 Input mci_08_year1 E4female -0.025380 0.383486 -1.171297 Input mci_09_year1 E4female 0.857854 -0.234353 -0.370665 Input mci_13_year1 E4male 0.121825 -0.495746 0.904760 Input mci_17_year1 E4male -0.466997 -0.044248 -0.776059 Input mci_18_year1 E4female 1.005059 -0.163064 -0.820915 Input mci_19_year1 E4male 1.152265 0.074567 -2.081952 Input mci_21_year1 E4female 0.121825 -0.091774 1.423562 Input mci_27_year1 E4female -1.350231 -0.543272 2.172568 Input mci_29_year1 E4male 1.888294 0.240908 0.683020 Input mci_35_year1 E4male 0.710648 -0.567035 1.014783 Input mci_41_year1 E4female 0.269031 0.169619 -0.510310 Input mci_42_year1 E4male 0.710648 -0.329405 -0.206476 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] glmfit error on v5.1
There you are!Hope it helps- Mensaje original -De: Douglas N Greve gr...@nmr.mgh.harvard.eduFecha: Lunes, 2 de Diciembre de 2013, 5:09 pmAsunto: Re: [Freesurfer] glmfit error on v5.1A: freesurfer@nmr.mgh.harvard.edu Can you send the matrix that it creates? On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer experts, Sorry for the inconvenience but I posted this message last week, but I did not receive any answer. I really need to keep going on with my analyses.I have runned the following command line: mri_glmfit --surf PLI_MCI_sample7_avg lh --C/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/ which is always prompts the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07 Possible problem with experimental designI'm sending attached the fsgd.txt and contras.mat files used in case you need themDoes anyone knows what's wrong with my design?Many thanks in advanced, Gabriel.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. font size="3"--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font Xg.dat Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] glmfit error
Dear FS experts I'm running glmfit with FS v5.1 and get the following error:ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07Possible problem with experimental designcommand line:mri_glmfit --surf PLI_MCI_sample7_avg lh --C /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/I've performed analyses like this many times, but with different subjects, more subjects but same fsgd structure (same regressors), and I have no Idea of what's wrong in here.Please, find attached the contrast and the fsgd matrices used.Can any one guide me on this?Many thanks in advanced,Gabriel contrast_withinE4_neg.mat Description: Binary data GroupDescriptorFile 1 Title PVEc-PET_with_MRI in sig_clusters of MC_3000 Class E4female Class E4male Class noE4female Class noE4male variables zAge zAPOB zlh.cortex_AVGthickness Input mci_01_year1 noE4male -0.025380 -0.495746 -0.569553 Input mci_02_year1 noE4male 0.416237 -0.163064 -1.388804 Input mci_04_year1 noE4female -0.466997 -1.018533 1.324541 Input mci_10_year1 noE4male -0.319792 -1.351215 0.286936 Input mci_11_year1 noE4female 0.563442 -0.400694 -0.384206 Input mci_14_year1 noE4male -0.466997 -0.281879 0.611082 Input mci_15_year1 noE4female 1.152265 -0.567035 0.446893 Input mci_16_year1 noE4male 0.857854 0.549827 -1.563149 Input mci_20_year1 noE4male -0.614203 -1.066059 -0.254717 Input mci_23_year1 noE4male 1.299471 -0.780902 -0.043134 Input mci_25_year1 noE4male -0.761409 -0.899718 0.469744 Input mci_33_year1 noE4male -0.908614 0.858747 0.584846 Input mci_36_year1 noE4male -0.025380 2.260766 -0.997798 Input mci_38_year1 noE4male -2.822288 2.759790 1.354163 Input mci_39_year1 noE4male -1.350231 2.569685 0.621238 Input mci_06_year1 E4female -0.172586 -0.234353 -0.633028 Input mci_07_year1 E4male -1.350231 -0.139301 -0.126075 Input mci_08_year1 E4female -0.025380 0.383486 -1.171297 Input mci_09_year1 E4female 0.857854 -0.234353 -0.370665 Input mci_13_year1 E4male 0.121825 -0.495746 0.904760 Input mci_17_year1 E4male -0.466997 -0.044248 -0.776059 Input mci_18_year1 E4female 1.005059 -0.163064 -0.820915 Input mci_19_year1 E4male 1.152265 0.074567 -2.081952 Input mci_21_year1 E4female 0.121825 -0.091774 1.423562 Input mci_27_year1 E4female -1.350231 -0.543272 2.172568 Input mci_29_year1 E4male 1.888294 0.240908 0.683020 Input mci_35_year1 E4male 0.710648 -0.567035 1.014783 Input mci_41_year1 E4female 0.269031 0.169619 -0.510310 Input mci_42_year1 E4male 0.710648 -0.329405 -0.206476 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] autorecon3 error
I'm re-sending an old problem, because I received no answer. Cheers, Gabriel - Mensaje original - De: Gabriel Gonzalez Escamilla ggon...@upo.es Fecha: Lunes, 10 de Junio de 2013, 4:56 pm Asunto: Re: [Freesurfer] autorecon3 error A: Bruce Fischl fis...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Dear Doug Sorry for late answer. I did open as: tksurfer qsm1_17 lh inflated, and then File load surface lh.sphere.reg and tksurfer qsm1_17 lh sphere.reg Neither of them look bad, it looks very spherical, an has nothing strange to my eyes... Any other ideas??? Best Regards Gabriel - Mensaje original - De: Bruce Fischl fis...@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggon...@upo.es CC: freesurfer@nmr.mgh.harvard.edu Hi Gabriel seems like something is wrong with that surface file. Can you load the lh.sphere.reg in tksurfer and see if it looks ok? Bruce On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]-v[1] = 539832625 - out of range! reading atlas from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] autorecon3 error
Dear Doug Sorry for late answer. I did open as: tksurfer qsm1_17 lh inflated, and then File load surface lh.sphere.reg and tksurfer qsm1_17 lh sphere.reg Neither of them look bad, it looks very spherical, an has nothing strange to my eyes... Any other ideas??? Best Regards Gabriel - Mensaje original - De: Bruce Fischl fis...@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggon...@upo.es CC: freesurfer@nmr.mgh.harvard.edu Hi Gabriel seems like something is wrong with that surface file. Can you load the lh.sphere.reg in tksurfer and see if it looks ok? Bruce On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]-v[1] = 539832625 - out of range! reading atlas from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] autorecon3 error
Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg /root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]-v[1] = 539832625 - out of range! reading atlas from /root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FS v5.3 release doubs
Dear FS experts, I have runned my xHemi analysis with FSv5.1, but you sent me the updates for this aproach when the FSv5.2 was available, does the xHemi analyses are affected by this thickness and area measures problem? Kind Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Permutation doubts
Dear Freesurfer experts,I'm having troubles when setting a permutation test, I'm making group comparisons, but I'm introducing the Age, and cortical thickness as niusance variables (as previously recommended).It seems that permutations only work for orthogonal matrices, does this means that I cannot set any niusance variable?If so, this is telling me that I can run the command with the flag --perm-force, and I'm wondering, which would be the implications of force to run the permutations with niusance variables?Many thanks in advance,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc with --xhemi
By real I was reffering to the interpretation differences of using the lh-rh diff maps or the LI maps.Bests,Gabriel.El 02/04/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:I don't know what you mean by real. Is the LI not real? The LI will remove the effect of scaling (eg, brain size).On 04/02/2013 04:48 PM, Gabriel Gonzalez Escamilla wrote: So, this means that the real differences is as Yizhou wrote? One measures the asymmetry (measured as the difference between lh-rh), and the LI or --paired-diff-norm will tell the extent of this asymmetry. Regards, Gabriel. El 02/04/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: sorry, I misspoke, the p-value will be different (perhaps very different) between LI and --paired-diff. The p-value should not change between LI and --paired-diff-norm; these two maps differ only by a scale which is removed in the t-ratio. doug On 04/02/2013 01:15 PM, Yizhou Ma wrote: If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff dougIn my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually.On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu wrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es mailto:ggon...@upo.es ggon...@upo.es ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output
Re: [Freesurfer] mris_preproc with --xhemi
Dear Doug,Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it?standardLI = (lh-rh)/(lh+rh)FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one.Further, this division should be done before the smoothing, right?If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps?Regards,Gabriel.El 29/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ...If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etcIf you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc.Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2.Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then runmri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mghIn my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet.dougOn 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc with --xhemi
sorry I meant to do the division, to standarize the LI after the smoothing.El 02/04/13, Gabriel Gonzalez Escamilla ggon...@upo.es escribió:Dear Doug,Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it?standardLI = (lh-rh)/(lh+rh)FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one.Further, this division should be done before the smoothing, right?If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps?Regards,Gabriel.El 29/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ...If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etcIf you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc.Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2.Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then runmri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mghIn my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet.dougOn 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc with --xhemi
So, this means that the real differences is as Yizhou wrote?One measures the asymmetry (measured as the difference between lh-rh), and the LI or --paired-diff-norm will tell the extent of this asymmetry.Regards,Gabriel.El 02/04/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:sorry, I misspoke, the p-value will be different (perhaps very different) between LI and --paired-diff. The p-value should not change between LI and --paired-diff-norm; these two maps differ only by a scale which is removed in the t-ratio.dougOn 04/02/2013 01:15 PM, Yizhou Ma wrote: If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? The p-value will not change since the LI is just a scaled version of the paired-diff doug In my opinion, the interpretation will be different, and the difference just depends on the difference between (lh-rh) and LI themselves. The former tells you if the lh is bigger than the rh in absolute values, while the latter tells you to what extent it is asymmetrical. The latter is not a scaled, but a standarized version of the former. Which you use in your study really depends on which you are interested in conceptually. On Tue, Apr 2, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu wrote: I think it is best to do it before the smoothing, though my results did not really change when I did it after. doug On 04/02/2013 12:07 PM, Gabriel Gonzalez Escamilla wrote: sorry I meant to do the division, to standarize the LI after the smoothing. El 02/04/13, *Gabriel Gonzalez Escamilla * ggon...@upo.es mailto:ggon...@upo.es ggon...@upo.es escribió: Dear Doug, Interesting but, if I'm understanding this well, to get a normal LI, the --paired-diff-norm should be divided by 2 not multiplied, isn't it? standardLI = (lh-rh)/(lh+rh) FS_LI = (lh-rh)/((lh+rh)/2) -- as you are dividing the denominator, your LI will be twice an standard one. Further, this division should be done before the smoothing, right? If I do use the LI maps to perform my stats, which would be the difference in interpretation between the results of using the --paired-diff maps, and the standarized LI maps? Regards, Gabriel. El 29/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu gr...@nmr.mgh.harvard.edu escribió: The --xhemi flag causes both the left and right hemispheres of each subject to be stacked into the output file. So the output file will have number of subjects x2 frames. The order is subject1.lh, subject1.rh, subject2.lh, subject2.rh, ... If you add the --paired-diff, then you will get number of frames = number of subjects, and each frame will be subject1.lh-rh, subject2.lh-rh, etc If you use the --paired-diff-norm instead, then you will get what you want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc. Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would need to multiply the paired-diff-norm by 2. Finally, I want to point out that it may be better to smooth before computing the LI because the LI computation is non-linear and it has the potential to divide by a noisy number. To do this, run without the --paired-diff flags, then smooth, then run mri_concat yourfile.smoothed.mgh --paired-diff-norm --o yourfile.smoothed.LI.mgh In my study, I ran it both ways and it did not make a difference, but I think smoothing before LI is the safer bet. doug On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote: Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the --xhemi flag do in the mris_preproc command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for --paired-diff, and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D
Re: [Freesurfer] Xhemi stat questions
That makes much more sense than the thing I was looking for.Now I have a problem reading the lh.lh-rh.thickness.mgh with the load_mgh.m function, as I have no idea of how to read it to get the vertex by vertex thickness value of each subject.I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubjs])then reading: subjIDthick=thick(vtxID,1,1,subjID);where vtxID es the vertex of the .label file I want, and subjID is the number of the subject.is that correct?All this is because I will use it as a covariate in the statistical analysis as suggested in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27129.htmlRegards,Gabriel.El 26/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Unless you specifically need them for an individual, you should get them from lh.lh-rh.thickness.mgh because that data is sampled onto the symmetric template and so should be unbiased (ie, it will not systematically favor lh or rh).dougOn 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I meant of a given subject, But, As I'm thinking about this, I'm wondering if it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals? I suppose that I should read the lh.lh-rh.thickness.mgh created by mris_preproc to get the average differences in lh-rh hemispheres. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym? doug On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject.Regards, GabrielEl 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. dougRegards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced
Re: [Freesurfer] Xhemi stat questions
Dear Doug,I meant of a given subject, But, As I'm thinking about this, I'm wondering if it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals?I suppose that I should read the lh.lh-rh.thickness.mgh created by mris_preproc to get the average differences in lh-rh hemispheres. Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym?dougOn 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values?B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de
Re: [Freesurfer] Xhemi stat questions
Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices?Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep?Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres?what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of:The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel.-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ /root/trabajo/freesurfer/bin/mris_preproc_old /root/trabajo/freesurfer/bin/mris_preproc 14,15c14,15 #$Date: 2012/12/06 16:06:52 $ #$Revision: 1.59.2.4 $ --- #$Date: 2012/12/06 16:06:17 $ #$Revision: 1.66 $ 32c32 set VERSION = '$Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $'; --- set VERSION = '$Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $'; 77a78 set DoXHemiOnly = 0; # do not include the non-xhemi 445a447,453 case --tal-xyz: if($#argv 1) goto arg1err; set svalsurf = $argv[1]; shift; set sval = tal-xyz set srcsurf = 1; breaksw 679a688,692 case --xhemi-only: set DoXHemi = 1; set DoXHemiOnly = 1; breaksw 923,924c936,941 if($srchemi == lh) set tmplist = ($tmplist $subj $subj/xhemi) if($srchemi == rh) set tmplist = ($tmplist $subj/xhemi $subj) --- if($DoXHemiOnly) then set tmplist = ($tmplist $subj/xhemi) else if($srchemi == lh) set tmplist = ($tmplist $subj $subj/xhemi) if($srchemi == rh) set tmplist = ($tmplist $subj/xhemi $subj) endif 1017a1035 echo --tal-xyz surfname : output xyz in mni305 for each subject 1109c1127 --area surfname --- --tal-xyz surfname ,1112c1129,1131 Extract vertex area from subject/surf/hemi.surfname to use as input. For use with --s, --fsgd, or --f
Re: [Freesurfer] Xhemi stat questions
Thank you, so I'm keeping the one I had.Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject.Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote:Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc.Those differences are just added features and won't change your results.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices?I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc.dougRegards,GabrielEl 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep?Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres?what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of:The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0Is the L-R difference between Grp1 and Grp2 different than 0 (regressingout Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0Is the L-R difference between Males and Females different than 0(regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5Does the slope of the L-R difference with Var1 differ between Grp1 andGrp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5Does the slope of the L-R difference with Var1 differ between Male andFemale(regressing out group) Many thanks in advanced. Gabriel.-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Xhemi stat questions
I mean of a given subject, I suppose that on the fsaverage_sym, I would read the lh.lh-rh.thickness.mgh. But, As I'm thinking about this, I'm wondering if it has sense, or if I should obtain the lh-rh thickness differences? Nevertheless, I have no idea how to get any of those measurements.Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym?dougOn 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values?B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es
[Freesurfer] Xhemi stat questions
Dear Doug,I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh?On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so:A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres?B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: 1) 5 .5 -.5 -.5 0 0 0 02) 5 -.5 .5 -.5 0 0 0 03) 0 0 0 0 .5 .5 -.5 -.54) 0 0 0 0 5 -.5 .5 -.5Many thanks in advanced.Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Gray matter
Hi Jordi,I think you are looking for the information contained on the wiki:http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStatsTotalGray - total gray matter volume. This is simply the sum of SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes both surface-based volume calculations and voxel counts. To get a volume.mgz for the GM, you can use matlab and the aseg.mgz, or mri_extract_label, both with the number-IDs of the corresponding labels, as found in FreeSurferColorLUT.txtCheers,Gabriel. El 22/03/13, Jordi Delgado jordi...@pic.es escribió:Dear FS experts,I have a double question about the gray matter calculations in FS:- Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this informationKind Regards, -- Jordi -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Stat doubts
Thanks Doug for your quick answer, Sorry for so late answer.One question about this, is about the fast_vol2mat, is this a function? if so, where can I get it?As the PCC is the R value, I'm guessing that I can just square at it, to obtain R2.When you asked me to divide the beta by
sqrt(rvar), is there any place where I can find is this is the correct way to get the standardized beta?Best regards,GabrielEl 14/03/13, Douglas Greve gr...@nmr.mgh.harvard.edu escribió:
Hi Gabriel, I've attached a matlab routine which will compute the
PCC. If you cd into the GLM dir, then
X = load('Xg.dat');
beta = MRIread('beta.mgh');
C = load('yourcontrast/C.dat');
rvar = MRIread('rvar.mgh');
betamat = fast_vol2mat(beta);
rvarmat = fast_vol2mat(rvar);
rhomat = fast_glm_pcc(betamat,X,C,rvarmat);
rho = beta;
rho.vol = fast_mat2vol(rhomat,rho.volsize);
MRIwrite(rho,'yourcontrast/pcc.mgh')
The R2 should just be the square of the PCC, right?
For the standardized beta, do you just divide the beta by
sqrt(rvar)?
doug
On 3/14/13 1:39 PM, Gabriel Gonzalez
Escamilla wrote:
Dear Freesurfers
I'm performing regression analyses including confounding
variables, and I would like to know how to obtain the following
information:
A) The squre R
and
B) The standarized beta coefficient of an independient variable;
and the partial correlation with its p-values
Many thanks in advanced,
Gabriel
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-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Stat doubts
Dear Freesurfers I'm performing regression analyses including confounding variables, and I would like to know how to obtain the following information:A) The squre Rand B) The standarized beta coefficient of an independient variable; and the partial correlation with its p-valuesMany thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] glmfit-sim trouble
Dear FreeSurfers,I'm running some simulations, I have two computers, with exactly the same configuration, but it works on one and not in the other.I run the mri_glmfit on one computer, and then copied the directories to the second computer in order to run the simulations.and it always ask for some disk partition of the first computer, even when the analyses were run on the same folder directories.In my two computers I have everything under: /root/trabajo/freesurfer/subjects/So I don't know why is it asking for another directory in the second computermy command to run with the simulations is: mri_glmfit-sim --glmdir my_dir --sim mc-z 2000 1.3010 mc-z.positive --sim-sign pos --cwpvalthresh 0.05Any ideas?Many thanks in advanced,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Xhemi questions
Thanks you for your quick answer Doug,Just one clarification, in the correction for multiple comparisons, which is the main difference between the mc-z and the permutation test? rather than making simultaions or working on original data. And Why is 5000 runs recommended to mc-z and 1 for permutation testing?Thanks,Gabriel.El 07/02/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:On 02/06/2013 12:49 PM, Gabriel Gonzalez Escamilla wrote: Dear Doug and FreeSurfer experts, Thnak you so much for all your lasts responses!. I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions: given the command for interhemispheric comparisons: mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh; A) This read all subjects to construct X and C as one-sample group mean, this means that as result I get the difference across hemispheres and across my subjects in a population, right?Correct. B) But, what if I have two groups? controls and patients, I'm wondering if is it possible to examine regional differences of thickness asymmetries between those two groups? or more?This just becomes a standard two group analysis as described in the tutorials. You create an FSGD file with two classes and list your input subjects. C) If I want to examine effects of group or sex, while controlling for age and other factors how do I introduce them into the glm model? If so, do I set the contrasts as normally for mri_glmfit? I mean as any other thickness study? or there is any other thing that I should do?You do not need to do anything different than with a normal thickness study. The command for multiple comparisons correction is: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 Which performs only cluster-wise corrections, D) is there any other way to correct for multiple comparisons, something like permutation tests or anything else?Yes, you can run something likemri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 --sim perm 1 2 csdperm --sim-sign absYou should run mri_glmfit-sim --help to see what these options mean as you may need to change the voxelwise threshold (the 2 value)doug Many thanks in advanced, Gabriel-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Xhemi questions
Dear Doug and FreeSurfer experts,Thnak you so much for all your lasts responses!.I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions:given the command for interhemispheric comparisons:mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh;A) This read all subjects to construct X and C as one-sample group mean, this means that as result I get the difference across hemispheres and across my subjects in a population, right? B) But, what if I have two groups? controls and patients, I'm wondering if is it possible to examine regional differences of thickness asymmetries between those two groups? or more?C) If I want to examine effects of group or sex, while controlling for age and other factors how do I introduce them into the glm model? If so, do I set the contrasts as normally for mri_glmfit? I mean as any other thickness study? or there is any other thing that I should do?The command for multiple comparisons correction is:mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 --cache 2 absWhich performs only cluster-wise corrections, D) is there any other way to correct for multiple comparisons, something like permutation tests or anything else?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Reenviar: xhemi registration problem
Nick,Is not the one from the distribution, is the one on the FS-xhemi wikihttp://surfer.nmr.mgh.harvard.edu/fswiki/XhemiIf I use the one from my the fs v5.1 distribution, will it work as the one on the wiki???Thanks,GabrielEl 31/01/13, Nick Schmansky ni...@nmr.mgh.harvard.edu escribió:Gabriel,Where did you get the mri_convert? Did it come with the installation? The GLIBC_2.4 error indicates that mri_convert was built on a newer OS,like Centos6, than the one you are running on. I'd recommend using ourcentos4 build of freesurfer.Nick Hello Bruce and Nick, I'm writing with the same topic from the last time, for which I haven't get aswered and I'm a stocked with it. Is about the FS inter-hemispheric registration. I'm sending you the threat so i don't make this mail too long... http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26317.html I've checked all existing threats about this topic, but I have found no solution... Many thanks in advanced, Gabriel___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Reenviar: xhemi registration problem
Hello Bruce and Nick,I'm writing with the same topic from the last time, for which I haven't get aswered and I'm a stocked with it. Is about the FS inter-hemispheric registration. I'm sending you the threat so i don't make this mail too long...http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26317.htmlI've checked all existing threats about this topic, but I have found no solution...Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] xhemi problem
Thanks Doug for your answerBut, always the first one ends properlysurfreg --s c_003 --t fsaverage_sym --lhit's the second one that have two different errors:surfreg --s c_003 --t fsaverage_sym --lh --xhemiAnd yes you are right, it says that it's because of the library but, the original mri_convert did't have that trouble. I have also tried to excecute the command xhemireg but didn't work either.Thanks,GabrielEl 28/01/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The second command is probably failing because the first command is failing. The 1st is failing because you don't have GLIBC 2.4. I'll have to leave that one for Nick or Zeke.dougOn 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote:Well there is actually two kinds of error:1) when I runsurfreg --s c_003 --t fsaverage_sym --lhand then:surfreg --s c_003 --t fsaverage_sym --lh --xhemisáb ene 26 21:09:21 CET 2013setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjectscd /root/root/trabajo/freesurfer/bin/surfreg --s c_003 --t fsaverage_sym --lh --xhemiLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxxhemi does not exist for c_003, running nowxhemireg --s c_003outdir is /root/trabajo/freesurfer/subjects/c_003/xhemiLogfile is /root/trabajo/freesurfer/subjects/c_003/xhemi/xhemireg.lh.log/root/trabajo/freesurfer/bin/xhemireg--s c_003$Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $sáb ene 26 21:09:21 CET 2013Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux/root/trabajo/freesurfer/subjects/c_003setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjectssáb ene 26 21:09:21 CET 2013sáb ene 26 21:09:21 CET 2013mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgz --keep-precision --no-save-regMatrix from regfile:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;movvol mri/orig.mgztargvol mri/orig.mgzoutvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgzregfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.datinvert 0tal 0talres 2regheader 0noresample 0interp trilinear (1)precision uchar (0)Gdiag_no -1Synth 0SynthSeed 1360182876Final tkRAS-to-tkRAS Matrix is:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;Vox2Vox Matrix is:-1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;ResamplingOutput registration matrix is identitymri_vol2vol donemri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgz --keep-precision --no-save-regMatrix from regfile:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;movvol mri/T1.mgztargvol mri/T1.mgzoutvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgzregfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.datinvert 0tal 0talres 2regheader 0noresample 0interp trilinear (1)precision uchar (0)Gdiag_no -1Synth 0SynthSeed 1359747149Final tkRAS-to-tkRAS Matrix is:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;Vox2Vox Matrix is:-1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;ResamplingOutput registration matrix is identitymri_vol2vol donemri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgz --keep-precision --no-save-regMatrix from regfile:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;movvol mri/brain.mgztargvol mri/brain.mgzoutvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgzregfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.datinvert 0tal 0talres 2regheader 0noresample 0interp trilinear (1)precision uchar (0)Gdiag_no -1Synth 0SynthSeed 1359336383Final tkRAS-to-tkRAS Matrix is:-1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;Vox2Vox Matrix is:-1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;ResamplingOutput registration matrix is identitymri_vol2vol donemri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003
Re: [Freesurfer] xhemi problem
0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/norm.mgz --targ mri/norm.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/norm.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/norm.mgz targvol mri/norm.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/norm.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1359823654 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/aseg.mgz --targ mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/aseg.mgz targvol mri/aseg.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1360101198 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.mgz /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.mgz --left-right-swap-label mri_convert: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by mri_convert)2) When I do reboot the computer and execute just the second one:surfreg --s c_003 --t fsaverage_sym --lh --xhemi sáb ene 26 19:30:39 CET 2013 setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjects cd /root /root/trabajo/freesurfer/bin/surfreg --s c_003 --t fsaverage_sym --lh --xhemi Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux #@# lh sáb ene 26 19:30:39 CET 2013 #CMD# mris_register -curv -annot aparc.annot /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere /root/trabajo/freesurfer/subjects/fsaverage_sym/lh.reg.template.tif /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.fsaverage_sym.sphere.reg using smoothwm curvature for final alignment zeroing medial wall in aparc.annot $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere... MRISread(/root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere No such file or directory El 25/01/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Can you send the command line and terminal output?On 01/25/2013 09:38 AM, Gabriel Gonzalez Escamilla wrote: Dear FS experts, I'm trying to perform the intrerhemispheric registration method on my centOS 4, I have downloaded all the files, but the mri_convert is saying that does not found the necessary libraries. I did download the mri_convert.linux, I have tried to re-download the file, but it apparentelly is not available anymore. Can any one help me? Many thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
[Freesurfer] xhemi problem
Dear FS experts,I'm trying to perform the intrerhemispheric registration method on my centOS 4, I have downloaded all the files, but the mri_convert is saying that does not found the necessary libraries. I did download the mri_convert.linux, I have tried to re-download the file, but it apparentelly is not available anymore.Can any one help me?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] WM of lobes
Dear freesurfersI'm trying to get the WM parcellation by lobes, I have read some previous FS archives regarding a similar topic, but they only want the volume value, and I'm interested in a WM lobes parcellation in mgz format (like aseg.mgz ), and I'm also interested in knowing if is possible to obtain this lobar parcellation for only cortical WM. Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] gca atlas creation
Dear FreeSurfer expertsHapp new year to all of you, and thanx for all your help along the past 2012.I would like to make some questions regardins a new atlas creation1) In a first step before mri_ca_train I did use mri_ca_normalize to normalize my FS_MNI152average subject to the JHU.ICBMtracts.1mm.mgz but this create an empty norm.mgz, is this normal? whean I saw that the norm.mgz was empty I decide to create all the files by:recon-all -s My_MNI152_avg -autorecon1 -autorecon2-inflate1, that create all files as normally does with my every other subjects; Then I run mri_ca_train, using as -mask the brain.mgz, as -T1 the norm.mgz created during recon-all, directed to my FS_MNI251average subject, and as -parc_dir JHU.ICBMtracts.1mm..mgz; as result got the .gca and a mgh fileI use the load_gca.m to check the .gca created, but get the next error message:version 5 in file $JHU.ICBMtracts_12_2012.gca incorrect - not a known gca file2) Is there any way to check at the gca file created? just to make myself sure that everything is placed in the right way3) And lastly, Which is the next step to parcellate the WM of all my subjects as the new atlas? Can I use this gca file with mris_ca_label? or some other tool will be better?Many thanks in advanced,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] new atlas
Dear Freesurfers,Sorry for so many and basic questions lately.I'm working with my set of subjects (T1), and I'm looking for a different WM parcellation than the aseg.mgz, I have an atlas (JHU atlas in MNI space, Mori et al 1999, and some other in Colin27 space).I'm guessing I will have to use the FSaverage subject as target space. Since FS has many algorithms to make registrations, and the mris_ca_train requieres the predefined labels into an anootation file. I'm wondering about the best way to translate all the WM labeling from this atlas into FS space. Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM-hypointensities
OK the Doug, I know which are the voxels contained into a ROI. From all of them I know the norm.mgz and the brainmask.mgz values, because I'm assuming that FS always work with the brainmask.mgz to know the actual voxel intensity, as indicated when running mri_segstats.I can easily calculate the mean of the norm voxel intensities, do I need anything else?Could you tell me the formula to compute the PV?Kind Regards,Gabriel.El 17/12/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:The PV is done based on intensities. For each voxel an the boundary of an ROI, the voxel intensity is assumed to be a weighted summation of the the average intensities in each ROI. Knowing the average intensities in the ROIs and the actual intensity of the voxel, the PV can be computed.dougOn 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote: Thanks Doug, In my case I did as you said but as Bruce recommend use the wmparc, so the voxels less than 4000, and = 5001 were left , and more than or equal to 4000, and =5002 were right. So different approach but I think would be the same, isn't it? Can you explain to me how FS makes the PV correction on the output volumes in aseg.stats? Best Regards, Gabriel. El 13/12/12, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: Gabriel, the way I've done it is to just assign WMSA to left or right based on the column number of the WMSA voxel. If it is less than 128, then it is right (78) if it is greater than 128 it is left (79). It's not perfect, but it is correct in the vast majority of cases. doug On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote: Thanks Bruce, The problem is that for this set of subjects I only have the T1s, anyways I would like to give a try onto the tools for WMSA, since I have T2 from some subjects. On the other hand, If I'm right the way to do the assignment on matlab, would be something like opening the mgz, finding their positions and look which are the neighbors right? If so, I would like to not assign just the neighbor voxel, as this might bias the assignment, I'm guessing that something like the assignment done during the aparc+aseg.mgz creation (using GM parcelation to map GM labels to the wm voxels - mri_aparc2aseg) should be a correct way to do so. Can you point me to an article or explain to me how this works indeed, and how the decision to the belonging voxel is made, I think I know the basis, but not enough to make my own script. If I do not understand bad, is something like, you take a voxel a look to some contiguous voxels till you get into a point where all the contiguous voxels are too far from the seed, and are surrounded by lots of voxels belonging to other areas. I'm not quite sure about the decision about when to stop the search. I really think that the method like the implemented in the mri_apar2aseg is the perfect solution. Regards, Gabriel El 12/12/12, *Bruce Fischl * fis...@nmr.mgh.harvard.edu escribió: then I would either use TRACULA (if you have DWI) or the wmparc to generate ROIs. I meant that you could count whether there are more lh or rh wm labels neighboring each one to figure out which hemi they are in cheers Bruce On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Yes I did loo at the total WH-hypointensities(77), and substract them without a problem. What do you mean with lateralize them based on neighboring labels? How can I perform such thing on FS? Actually I'm interested in knowing to wich specific label o region they are. Bests, Gabriel El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió: Hi Gabriel we don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels. cheers Bruce On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers, I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it. Can any one help me? Best Regards, Gabriel. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http
[Freesurfer] left/right WM vols
Dear FreeSurfer expertsI'm trying to study WM-lesions of my data. As I saw in previous messages to the forum and papers, it is contained in the aseg.mgz as the WM-hypointensities volume (label-ID 77), but it has only one value from the whole brain in the aseg.mgz, the left/right fields appear empty in the aseg.stats, and I would be interested in subtract this volume value, or volume label image for each hemisphere. Is it possible on FS? May thanks in advanced,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] WM-hypointensities
Dear Freesurfers,I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it.Can any one help me?Best Regards,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM-hypointensities
Yes I did loo at the total WH-hypointensities(77), and substract them without a problem.What do you mean with lateralize them based on neighboring labels? How can I perform such thing on FS?Actually I'm interested in knowing to wich specific label o region they are.Bests,GabrielEl 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielwe don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels.cheersBruceOn Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:Dear Freesurfers,I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty inthe aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it.Can any one help me?Best Regards,Gabriel.The information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM-hypointensities
Thanks bruce, for your answer,Does it exist a tool on FS or matlab to do such asignment of voxels from the WM-hypointensities (77) to the neighbouring labels?If so, does it can use whoever the aseg.mgz,the aparc+aseg or the wmparc.mgz to do this asignment?Thanks,GabrielEl 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielwe don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels.cheersBruceOn Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers, I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it. Can any one help me? Best Regards, Gabriel. ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] registration Fail
Dear Fresurfer experts,I have extract some labels from the aseg into a volume file. I want to export these labels of each subject into a template, such as FSaverage or myAverage subject.I've tried to create a register a matrix from the orig.mgz on the individual space to the orig.mgz on myAverage subject, but there are some displacements, and depending of the subject, the registration is not good at all. I create the register matrices with: mri_vol2vol, tkregister2 and bbregister, and non of these gave me the expected result. But mri_vol2vol, showed the best results.Can any one help me with this?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] wm vol mismatch
I understand, so i will use this images, but can you recommend me a good way to change my new volume file to a average subject space?I have tried registering the orig.mgz from the individual to the average using tkregister, mri_vol2vol, and bbregister, getting not good results at all.Any suggestions?Best Regards,Gabriel.El 21/11/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Hi Gabriel, this is normal. The volumes listed with aseg.stats have been corrected for partial volume, so it is not as simple as counting up all the voxels.dougOn 11/21/2012 12:36 PM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer, I'm trying to convert come labels from the aseg.mgz into nifti volumes I'm using: mri_extract_label aseg.mgz # and aseglabel#.nii where the # is the label as appears on the freesurferColoLUT.txt and it seems to work perfectly, but the number of voxels does not match with the number of voxels output in the aseg.stats, is this normal? they vary from i.e. 2603 in the aseg.stats to 2466 in the volume. to verify that it was't a problem from the extraction, I have tryed mris_binarize to match the same # segID as the mri_extract_label, and also use the matlab functions to open the aseg.mgz and keep those voxels which value were close to the #. With these two new options I get exactly the same number of voxels as with mri_extrac_label. So I don't know what could be the problem. Does anyone have an idea? Best Regards, Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer@nmr.mgh.harvard.edu
Dear DougI'm looking for making the interhemispheric registration procedure of FS, I was just gertting familiar with it by reading the:http://surfer.nmr.mgh.harvard.edu/fswiki/XhemiI found that in the step # Correct for MC say that this need a new version of mri_glmfit-sim, is this version somehow available now? or it does refeer to the FS v5.1 version?I have two doubs about the whole procedure:which are the main differences between using the FS average and creating my own average?and second: if I decide to create my own atlas, after all the 1.3 procedure, should I then run the 1.2 steps subtituing the FSaverage_sym for mine?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] wm vol mismatch
Dear Freesurfer,I'm trying to convert come labels from the aseg.mgz into nifti volumesI'm using: mri_extract_label aseg.mgz # and aseglabel#.nii where the # is the label as appears on the freesurferColoLUT.txtand it seems to work perfectly, but the number of voxels does not match with the number of voxels output in the aseg.stats, is this normal?they vary from i.e. 2603 in the aseg.stats to 2466 in the volume.to verify that it was't a problem from the extraction, I have tryed mris_binarize to match the same # segID as the mri_extract_label,and also use the matlab functions to open the aseg.mgz and keep those voxels which value were close to the #.With these two new options I get exactly the same number of voxels as with mri_extrac_label. So I don't know what could be the problem. Does anyone have an idea?Best Regards,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] volume conversion problem
Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it.I'm doing everything with the a to d stepsa) cd /root/trabajo/freesurfer/subjects/s00x/mri/b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheaderc) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgzd) mri_convert -odt float brainraw.mgz brain.niibut in step b always get the following error:mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheadermovvol brain.mgztargvol rawavg.mgzoutvol brain2raw.mgzinvert 0tal 0talres 2regheader 1noresample 0interp nearest (0)precision float (3)Gdiag_no -1Synth 0SynthSeed 1352942991MRIalloc: could not allocate -512234304 frameCannot allocate memoryAny ideas how to solve this?Should I to re-run any recon?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] volume conversion problem
Here yu are:mri_info brain.mgzVolume information for brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 11.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWNras xform present xform info: x_r = -1., y_r = -0., z_r = 0., c_r = 2.1879 : x_a = -0., y_a = 0., z_a = 1., c_a = 11.6591 : x_s = -0., y_s = -1., z_s = -0., c_s = -17.2780talairach xfm :Orientation : LIAPrimary Slice Direction: coronalvoxel to ras transform: -1. -0. 0. 130.1879 -0. 0. 1. -116.3409 -0. -1. -0. 110.7220 0. 0. 0. 1.voxel-to-ras determinant -1ras to voxel transform: -1. 0. 0. 130.1879 0. -0. -1. 110.7220 -0. 1. -0. 116.3409 0. 0. 0. 1.mri_info rawavg.mgzMRIalloc: could not allocate -512234304 frameCannot allocate memoryAs I see, the problem comes from the rawavg.mgz, if I do convert the dicoms into mgz, would this solve the problem, right? or there's anything else I can do?Regards,GabrielEl 12/11/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Can you send the result ofmri_info brain.mgzmri_info rawavg.mgzdougOn 11/12/2012 10:27 AM, Gabriel Gonzalez Escamilla wrote: Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it. I'm doing everything with the a to d steps a) cd /root/trabajo/freesurfer/subjects/s00x/mri/ b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader c) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgz d) mri_convert -odt float brainraw.mgz brain.nii but in step b always get the following error: mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader movvol brain.mgz targvol rawavg.mgz outvol brain2raw.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1352942991 MRIalloc: could not allocate -512234304 frame Cannot allocate memory Any ideas how to solve this? Should I to re-run any recon? Many thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Comparing thickness at vertex level
Dear FreeSurfer experts,I'm wondering if is it possible to make vertex to vertex comparisons for thickness on a group of subjects. In other words, I have a bunch of subjects pre-processed with FS but I would like to make comparisons finding the thickness values at same vertex in all of them. Is this possible with Freesurfer?Given that at the beggining all they have different head/brain sizes, I was thinking that a regristration of the surfaces to the same space (FSaverage) would re-sample my data to match in number of vertex. for this, I think that maybe mri_surf2surf is capable of such a thing, and then I would have to search for each vertex, or optionally mris_preproc using the -target FSaverage flag would perform something similar. Please tell me what you think about this?Many thanks in advanced,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] withe matter of cortical Lables
Thanks Doug,I did create my own ctab and works perfectly!Regards,GabrielEl 18/10/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Hi Gabriel, don't use the ASegStatsLUT.txt ctab file. It will only report the volumes of structure in the ctab, and that ctab does not have the WM parcellations. You can use FreeSurferColotLUT.txt instead. When you use --empty, this will report on *everything* in the ctab, which will probably be overwhelming. If you run it without --empty, then some subjects may have a different number of structures. The only alternative is to create your own ctab with only the structures you are interested in.dougOn 10/17/2012 02:36 PM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer Experts Sorry for many mail, but I'm working on may things at the time. Apart from my corticalGM problems I'm trying to obtain the WM volumes from some regions in the apparc.annot such as precuneus, for this I'm using mri_aparc2aseg --s MySubj --labelwm --annot aparc --o /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz to convert the apparc into a volume file, and then obtaining such voxels correponding to the asigned WM using: mri_segstats --seg /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz --sum /root/trabajo/freesurfer/subjects/MySUbj/stats/Newaparc+aseg.stats --pv /root/trabajo/freesurfer/subjects/MySubj/mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in /root/trabajo/freesurfer/subjectsMySubj/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject MySubj the problem is that even when it seems to work, some of the structures have no WM volume in the stat table, but they do have assigned voxels on the Newaparc+aseg (see attached image), Is there something I've been doing wrong? the command gives me the same results when I use the aparc+aseg.mgz created during recon-all process. Can anyone guide me? Best Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] local GI calculation Error
Dear FS expertsI'm trying to calculate the local GI of my subjects but I'm having trouble with one of them, When I run recon-all -s MySubject -localGI it always give me the same message:... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012When I checked the mris_euler_number on the pial surface I get no topological defect:[root@localhost surf]$ mris_euler_number lh.pialeuler # = v-e+f = 2g-2: 134601 - 403797 + 269198 = 2 -- 0 holes F =2V-4: 269198 = 269202-4 (0) 2E=3F: 807594 = 807594 (0)total defect index = 0Also try as: mris_compute_lgi --i lh.pial --echoAnd get the following message: ... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.endifendifecho echorm -f ${MLF}rm -f /tmp/clgi_15928_.mif ( $RunIt ! -e ${tmpdir}/${input}_lgi.asc ) thenif ( 1 ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) thenecho ERROR: compute_lgi did not create output file '${tmpdir}/${input}_lgi.asc'!echo ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!exit 1exit 1The right hemisphere works perfectly...with this last command, but left just does not work.Any ideas about this? any way to fix it??? Can anyone help me?Best Regards,Gabriel
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Re: [Freesurfer] local GI calculation Error
Thanks Marie,Yes at the end I found a threat with the same problem and saw the solution, so I did the recon and re-run the GLI and worked fine, but i didn't re-run the -autorecon3, I would run this separately, I guess it will cause no problems. Regards,GabrielEl 19/10/12, Marie Schaer marie.sch...@unige.ch escribió:Hi Gabriel,It may be the case that because of the surface topology, the lGI fails on one vertex. Most of the time, just recomputing the surface creation solves the problem. Can you try to run recon-all -autorecon2-wm -autorecon3 -randomness -hemi lh -s c_36 and then rerun the lgi computation on this hemisphere?It should solve the problem. Let me know,Marie On Oct 19, 2012, at 3:43 PM, Gabriel Gonzalez Escamilla wrote:Dear FS expertsI'm trying to calculate the local GI of my subjects but I'm having trouble with one of them, When I run recon-all -s MySubject -localGI it always give me the same message:... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012When I checked the mris_euler_number on the pial surface I get no topological defect:[root@localhost surf]$ mris_euler_number lh.pialeuler # = v-e+f = 2g-2: 134601 - 403797 + 269198 = 2 -- 0 holes F =2V-4: 269198 = 269202-4 (0) 2E=3F: 807594 = 807594 (0)total defect index = 0Also try as: mris_compute_lgi --i lh.pial --echoAnd get the following message: ... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.endifendifecho echorm -f ${MLF}rm -f /tmp/clgi_15928_.mif ( $RunIt ! -e ${tmpdir}/${input}_lgi.asc ) thenif ( 1 ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) thenecho ERROR: compute_lgi did not create output file '${tmpdir}/${input}_lgi.asc'!echo ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!exit 1exit 1The right hemisphere works perfectly...with this last command, but left just does not work.Any ideas about this? any way to fix it??? Can anyone help me?Best Regards,Gabriel
___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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[Freesurfer] Problem with cortical GM vol
Dear FreesurfersAs recommended I'm calculating the cortical GMWM vols from the surfaces. Using the --excl-ctxgmwm to exclude the GMWM volume from the segmentations and the --surf-ctx-vol and --surf-wm-vol to respectively compute the GM and WM surface volumes. The problem is that in the aseg.stats file the lines:# surface-based-volume mm3 lh-cerebral-white-matter # surface-based-volume mm3 lh-cerebral-cortex # surface-based-volume mm3 rh-cerebral-white-matter# surface-based-volume mm3 rh-cerebral-cortex are not appearing, I've checked with the volumes using mris_volume -v lh/rh.pial and mris_wm_volume subjID lh/rh -v. Only the volumes from the mris_wm_volume coincide with the ones in the ones in the lines: # Measure lhCorticalWhiteMatter,.,Left Hemisphere Cortical White Matter Volume, ,mm3 in both hemispheres but not the cortical GM volumes-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problem with cortical GM vol (complete)
For some reason I'd send the las e-mail unfinished, here's the complete one:Dear FreesurfersAs recommended I'm calculating the cortical GMWM vols from the surfaces. Using the --excl-ctxgmwm to exclude the GMWM volume from the segmentations and the --surf-ctx-vol and --surf-wm-vol to respectively compute the GM and WM surface volumes. The problem is that in the aseg.stats file the lines:# surface-based-volume mm3 lh-cerebral-white-matter # surface-based-volume mm3 lh-cerebral-cortex # surface-based-volume mm3 rh-cerebral-white-matter# surface-based-volume mm3 rh-cerebral-cortex are not appearing, I've checked with the volumes using mris_volume -v lh/rh.pial and mris_wm_volume subjID lh/rh -v. Only the volumes from the mris_wm_volume coincide with the ones in the ones in the lines: # Measure lhCorticalWhiteMatter,.,Left Hemisphere Cortical White Matter Volume, ,mm3 in both hemispheres but not the cortical GM volumes.In fact for GM the volumes are: aseg.stats lh=156531.224634 rh=153692.917345mris_volue lh=436143.018321 rh=444925.772579Which as you may see are completely different, the sum from the two from the aseg are not even close to a single from the mris_volumeIs there any way to know which volumes are correct?and how can I calculate this to appear on my aseg.stats? or any other text fileMany Thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error measuring LGI
Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working.I'm using currently version of FS and matlab R2009b.the following error alwais apair:INFO: FreeSurfer build stamps do not matchSubject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjectsActual FREESURFER_HOME /root/trabajo/freesurfer-rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.logLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux/root/trabajo/freesurfer/subjects/c_Macarena/surf##@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pialERROR: Matlab is required to run mris_compute_lgi!Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012Matlab exist on the startup.m file as:% FreeSurfer -%fshome = getenv('FREESURFER_HOME');fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome);path(path,fsmatlab);clear fshome fsmatlab;%-%Can anyone help me on this?Best Regards,Gabriel
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Re: [Freesurfer] error measuring LGI
Thanks Marie,You are right is pointing to the FSmatlab directory not to the installation folder, but the wiki say so:You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script. Do I need to change that in the startup.m?I did also try the getmatlab command and said that matlab does not exist, I'm guessing this is the problem.Bests,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory.You can check using the command getmatlab.Let me know,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es wrote: Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working. I'm using currently version of FS and matlab R2009b. the following error alwais apair: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux /root/trabajo/freesurfer/subjects/c_Macarena/surf # #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012 Matlab exist on the startup.m file as: % FreeSurfer -% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-% Can anyone help me on this? Best Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] error measuring LGI
Dear Marie,I've tried to set the matlab installation path, into the tcsh path (where my FS_HOME is), but It's not working. I have no idea how to change this on the startup.m, can you help me with it?Regards,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory.You can check using the command getmatlab.Let me know,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es wrote: Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working. I'm using currently version of FS and matlab R2009b. the following error alwais apair: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux /root/trabajo/freesurfer/subjects/c_Macarena/surf # #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012 Matlab exist on the startup.m file as: % FreeSurfer -% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-% Can anyone help me on this? Best Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] error measuring LGI
Marie,I'm working on centOS 4, I'd add the path to the matlab installation folder on my PATH as:setenv MATLABPATH /root/trabajo/matlab2009
setenv PATH ${MATLABPATH}/bin:${PATH}And this is not working stillAny ideas?GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,I would start by adding the path to the matlab installation directory to $PATH. On a Mac it looks like /Applications/Matlab_R*/bin. Then the getmatlab command should work, and LGI as well.MarieOn 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla ggon...@upo.es ggon...@upo.es wrote:Thanks Marie,You are right is pointing to the FSmatlab directory not to the installation folder, but the wiki say so:You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script. Do I need to change that in the startup.m?I did also try the getmatlab command and said that matlab does not exist, I'm guessing this is the problem.Bests,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch marie.sch...@unige.ch escribió:Gabriel,If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory.You can check using the command getmatlab.Let me know,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es ggon...@upo.es wrote: Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working. I'm using currently version of FS and matlab R2009b. the following error alwais apair: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux /root/trabajo/freesurfer/subjects/c_Macarena/surf # #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012 Matlab exist on the startup.m file as: % FreeSurfer -% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-% Can anyone help me on this? Best Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.esggon...@upo.es ggon...@upo.eshttp://www.upo.es/neuroaging/es/
-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] Hippocampus Doubt
Thanks BruceYes and no, we did sum all the outputs from the subfields segmentation, but I didnot find the fornix, Is it included I. The fimbria? What would be the difference if I do not include this label? And what do you mean with different definitions of what's and is not included?Regards,GabrielEl 12/07/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabriel,certainly they won't match as (a) they are different algorithms, and (b) they are different definitions of what is and is not included. Did you sum up things like fimbria and fornix in your subfield totals?cheersBruceOn Thu, 12 Jul 2012, Gabriel Gonzalez Escamilla wrote:Hello,after applying hippocampal subfield segmentation to our sample, we noted that summation of hippocampal subfields (in mm3) differs considerably from hippocampal volume (derived from aseg) in some of our subjects:case 1: 2592 mm3 (aseg hipp. volume) versus 2116 mm3 (summation of hipp. subfields)case 2: 4764 mm3 (aseg hipp. volume) versus 4002 mm3 (summation of hipp. subfields)case 3: 1914 mm3 (aseg hipp. volume) versus 2110 mm3 (summation of hipp. subfields)Please let me know why this is happening, and if this mismatching can be considered normal.Thank you very much in advance.Best regards,GabrielThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampus Doubt
Hello,after applying hippocampal subfield segmentation to our sample, we noted that summation of hippocampal subfields (in mm3) differs considerably from hippocampal volume (derived from aseg) in some of our subjects:case 1: 2592 mm3 (aseg hipp. volume) versus 2116 mm3 (summation of hipp. subfields)case 2: 4764 mm3 (aseg hipp. volume) versus 4002 mm3 (summation of hipp. subfields)case 3: 1914 mm3 (aseg hipp. volume) versus 2110 mm3 (summation of hipp. subfields) Please let me know why this is happening, and if this mismatching can be considered normal.Thank you very much in advance.Best regards,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal subfield segmentation error
Hello,I got the following error in one of my subjects when running hippocampal subfields segmentation (only for the left hemisphere). Could you help me to solve this problem?maximalDeformation: 75.1793 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... numberOfEntries: 24131/root/trabajo/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 23175 Segmentation fault kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt failed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul 3 15:54:39 CEST 2012Thank you very much in advance.Best regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] hippo_subfields questions
Dear Fresurfer experts and Koen Van LeemputI have made the hippocampal subfield segmentation of a group a subject in which is supposed to take the hippocampus from the aseg segmentation and calculate the new subfields segmentations inside this hippocampus of each hemisphere, am I right?If so, The volumes between the aseg and the summed subfields are supposed to be nearly the same,I have checked the volume outputs from both the aseg and the subfield segmentations, but even when some of them seem to change subtely, some others seem to be quite different, more than I did expect. Here are some examples:summ-segmentaseg -- Volume in 1mm^3 2696.63932660 -- this difference is the lowest I'd get ~37 2116.854 2592 -- aseg volume greater than summed volumes from subfields ~4754002.35354764 -- aseg volume greater than summed volumes from subfields ~7622110.32351914 -- summed volumes from subfields greater than the aseg vol ~196I'm just wondering if this is normal, or if it could be some kind of trouble when making the subfield segmentations of my subjects? can any one exaplain to me why the differences can be so random between my subjects?Many thanks in advanced,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal segmentation doubts
Thank you so much for your answer Koen,I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.I have tried to perform the hippocampal subfields segmentation by running:recon-all -s MySubject -hippo-subfields and also:kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults But I always get the following error:maximalDeformation: 75.1793Transforming meshDone transforming meshRasterizing Levenberg-Marquardt...numberOfEntries: 24131/root/trabajo/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 23175 Segmentation fault kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtfailed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul 3 15:54:39 CEST 2012For more details, see the log file /root/trabajo/freesurfer/subjects/MySubject/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingThe recon-all.log says:##@# Hippocampal Subfields processing Tue Jul 3 15:48:33 CEST 2012 mkdir -p /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul 3 15:54:39 CEST 2012To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting This error occurres only on this subject and for the left hemisphere, not like this for the right hemisphere, which ends perfectly when running the second command. I'm sending you the configurationFileDeformation for the left hemisphere, in case it may help. Any help will be so appreciatedBest Regards,GabrielEl 04/07/12, Koen Van Leemput k...@nmr.mgh.harvard.edu escribió:Hi Gabriel,1. Using pre-processed data obtained with an older version ofFreeSurfer should be OK, as long as you remember that the obtainedresults might/will be different from the ones you'd get if you had runthe whole analysis from scratch.2. The generic label hippocampus is used to denote the tail of thehippocampus, where no attempt is made to further subdivide between thedifferent subfields. This is admittedly not a great naming convention- sorry for the confusion.3. You should not do any correction on the obtained volumes: partialvolume here merely means the effect of voxels containing a mix ofdifferent subfields simultaneously. The non-partial volume resultshere only indicate that this effect is not explicitly modeled when youcall the hippocampal subfield segmentation routine with its defaultsettings.Hope this helps,KoenOn Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamillaggon...@upo.es wrote: Dear Freesurfer experts I'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts... If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields? I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right? second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e. volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissure c_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626 and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced, Gabriel -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient
[Freesurfer] Hippocampal segmentation doubts
Dear Freesurfer expertsI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissurec_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced,Gabriel -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal segmentation
Dear FreesurfersI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissurec_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Volume to surface
Thank you Anderson,It looks like do just what I want to do, but I'm having a problem, I've give the permissions to make the file an executable as follows chmod +x /root/freesurfer/bin/aseg2surf but when I call it always say that bash: aseg2surf: command not found. My FS v5.1 is working properly and Actually as you can see I'd put the script you sent me into the bin folder on the $FREESURFER_HOME directoryRegards,GabrielEl 07/05/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Volume to surface
Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it.Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time:[root@localhost] srf2obj aseg_004.srf aseg_4.objgawk: /root/freesurfer/bin/srf2obj:2:' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards,GabrielEl 07/05/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Volume to surface
Anderson, I'm downloading using a windows computer (but I always do like that with every single script), which automatically recognizes the scripts as txt files and add the extension, could you send me a link to the downloading page? That way I can try again and see what happens. I did check in my Linux distribution and is just as you said, the gawk is the default, so I have no any other idea for this.Regards,GabrielEl 08/05/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Gabriel, This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and its explicit use only makes a difference for Mac users, who have to get it from MacPorts or Fink. Also, the first script should work with bash. The sh can be ash, dash or even other depending on the system, being all with less features than bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may work with any, but this isn't always the case. All the best! Anderson On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote: Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it. Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time: [root@localhost] srf2obj aseg_004.srf aseg_4.obj gawk: /root/freesurfer/bin/srf2obj:2: ' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards, Gabriel El 07/05/12, Anderson Winkler andersonwink...@hotmail.com andersonwink...@hotmail.com escribió: Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension. Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate. Hope it helps! All the best, Anderson On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: Hello all FS users and experts, I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands: First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first... Many Thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
Re: [Freesurfer] Volume to surface
Hi Anderson,Now everything works perfectly, thank you so much!!!Best Regards,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Volume to surface
Hello all FS users and experts,I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file,For this I'm using the next commands:First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.niiTo preserve the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mghAnd last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.ascI'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first...Many Thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Volume to surface 2
I did forget to tell you that when I use the last command it always outputs the following error:ERROR: MRISread: cannot read surface data from file lh.aseg2raw.mgh! It gives me the same error when trying to load the surface into tksurfer, Is that I've made something wrong?Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] OBJ conversion
Dear Anderson, I have seen this message and I'm currently trying to use your script srf2obj to convert to obj format some surfaces created by FS, firstly i did convert the aseg into a volume in the native space using mri_convert, after that, i'd transform the aseg volume into a surface mgh format (mri_vol2surf), then store the surface as ascii by using mri_convert then I'm using your script to convert that surface to an object file but always renturns the following error:aplication srf2objgawk: /root/trabajo/freesurfer/bin/srf2obj:2:' inválido en la expresiónrfer/bin/srf2obj:2: ^ caracter 'I'm working under centOS 4.3 Best Regards,GabrielEl 22/02/12, Anderson Winkler andersonwink...@hotmail.com escribió: Hi Darshan, If you'd like to go directly from FreeSurfer .asc to OBJ, the attached little script should do the trick... Hope it helps! All the best, Anderson On 21/02/12 16:59, Pedro Paulo de Magalhães Oliveira Junior wrote: There's a how-to in the FreeSurfer website: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo Pedro Paulo Jr. On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler manfr...@nmr.mgh.harvard.edu manfr...@nmr.mgh.harvard.edu wrote: Hi Darshan, as Bruce suggested, you can use mris_convert to get an STL file which you can import into Blender or MeshLab. Both write Wavefront OBJ files. - Manfred On 02/20/2012 07:24 PM, Darshan P wrote: Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Manfred G. Kitzbichler, Research Fellow Harvard Medical School Mass General Hospital Martinos Center for Biomedical Imaging 149 Thirteenth Street, Rm 10.018 Charlestown, MA 02129, USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] labels export
And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels?Regards,GabrielEl 24/04/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:they are just ascii files so it should be easy enough to do yourselfOn Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote:Thanks Priti,I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?Regards,GabrielEl 24/04/12, Priti Srinivasan rspr...@nmr.mgh.harvard.edu escribió: Hi Gabriel, Have you tried mri_label2vol? If you want the volume in the anatomical space: mri_label2vol --label labelname.label --temp T1_template.nii.gz --identity --o volumename.nii.gz If you want it in some other space, you can specify the registration matrix using --reg and the template using --temp. Hope that helps, Priti div style=font-family: 'Times New Roman'; font-size: 16px; divHello FreeSurfers,/divdivbr //divdivDoes any one of you know if exist a function to export labels as a ROI format?/divdivbr //divdivRegards,/divdivGabriel/div/divdivbr /-- br //divdivfont size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font/div ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] labels export
Hello FreeSurfers,Does any one of you know if exist a function to export labels as a ROI format?Regards,Gabriel-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] labels export
Thanks Priti,I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?Regards,GabrielEl 24/04/12, Priti Srinivasan rspr...@nmr.mgh.harvard.edu escribió:Hi Gabriel,Have you tried mri_label2vol?If you want the volume in the anatomical space:mri_label2vol --label labelname.label --temp T1_template.nii.gz--identity --o volumename.nii.gzIf you want it in some other space, you can specify the registrationmatrix using --reg and the template using --temp.Hope that helps,Priti div style=font-family: 'Times New Roman'; font-size: 16px; divHello FreeSurfers,/divdivbr //divdivDoes any one of you know if exist a function to export labels as a ROI format?/divdivbr //divdivRegards,/divdivGabriel/div/divdivbr /-- br //divdivfont size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font/div ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM modification
Hi Doug,I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message:mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats).Does this is normal, since the same FS version was running perfectly just before changing the mri_segstats file.I have search the lib.so.6 and I have it, but not sure about the GLIBC_2.4 do you know how can i check it? or where can I find it for my centOS distribution?Bests,GabrielEl 17/04/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linuxThe only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot.dougOn 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM modification
I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message:mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats).Does this is normal, since the same FS version was running perfectly just before changing the mri_segstats file.I have search the lib.so.6 and I have it, but not sure about the GLIBC_2.4 do you know how can i check it? or where can I find it for my centOS distribution?Bests,GabrielEl 17/04/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linuxThe only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot.dougOn 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM modification
Thanks Doug,Could you recommend me some kind of software or procedure to quantify lesion on my images?Regards,GabrielEl 17/04/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linuxThe only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot.dougOn 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] WM modification
Dear freesurfers,May be a silly question:I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29Is there any output on FS that quantifies the lesions as volume or something like?When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ?Could you guide me on this?Many thanks in advanced,Gabriel.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Gcut contrast change
Yes, thanks BruceI'd checked the intensity values, and they were exactly the same as before the skull strippingRegards,GabrielEl 09/04/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielthe contrast probably isn't changed, just the display. Tkmedit tries to compute good window level settings based on the image content, and after stripping there will be far less bright fat, so the brain will probably look brighter. Check the actual voxel values.cheersBruceOn Mon, 9 Apr 2012, Gabriel Gonzalez Escamilla wrote: Dear FreeSurfer experts I'm using the command recon-all -skullstrip -clean-bm -gcut -subjid name to improve the skull stripping of my subjects, but after running this command the contrast looks so changed (bright), is it normal? Does this whitening somehow can change the later analyses? Regards, Gabriel. ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Gcut contrast change
Dear FreeSurfer expertsI'm using the command recon-all -skullstrip -clean-bm -gcut -subjid name to improve the skull stripping of my subjects, but after running this command the contrast looks so changed (bright), is it normal? Does this whitening somehow can change the later analyses?Regards,Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] About new FS version
Dear FS experts I've seeing that a new version of FS is about to be realized, but I'm wondering how soon will be it.Bests,Gabriel-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
