[Freesurfer] R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity
Hi list, in the previous mail you have suggested to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in $SUBJECTS_DIR/subject/mri). I have two question please.A- my mask is on vmPFC, thus it include the both hemispheres. Should I divide it in right and left? If yes, how can I do?B- I have difficulties to run the fcseed-conf command:fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s SessXXX -cfg mean.ROI_MASK.configIs these command lines corrected? Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 13-lug-2015 10.16 A: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity Hi list, When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem to correspond. However, when I added the ROI_MASK.nii.gz, the orig is vanished, and is remained the ROI_MASK in correct position (and in white) and around all black. My concern is the correct binarization of ROI_MASK which it seem correct when I use fslview.fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs. After mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o func.vmPFC_MASK.nii The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with tkmedit and too big (a red bar which cover the whole) when I use fslview.With MRIcron, is screen is irregularly divided in half in black and white. Which should be the advised folder for func.vmPFC_MASK.nii? Thank you very much Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 30-giu-2015 0.36 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity Hi Stefano, sorry for the delay, I was traveling. It sounds like you just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask is in the orig.mgz space, then everything should work ok, but you can look at it with tkmedit -f orig.mgz -aux ROI_MASK.mgz You can also run mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o func.ROI_MASK.nii where template.nii.gz and register.dof6.dat are in the functional run folder doug On 06/12/2015 04:39 PM, std...@virgilio.it wrote: Hi list, I working on the combination of MRS and FS-FAST analysis. I have extracted the grey matter within voxel (I will call it ROI_MASK) by using FSL tools and now it is in the same space of orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I use fslview). I'd like to import it to FS for performing seed-based FS-FAST functional connectivity. The seed should the ROI MASK (GM within voxel). I know that the FSL and FS operate in different space and orientation. I think to have resolved the problem of different space by using orig.nii.gz to create ROI mask by FSL. However, I'm strongly worried for orientation issues. I have read the guidelines in FSL and FS sites, but I'm quite confused. In detail, I'd like to ask whether I should use mri_cor2label to transform ROI mask created by FSL to label. Furthmore, I'd like to be sure of the position of the ROI. How can I visualize it to be sure that the seed of my FS-FAST analysis is effectively the my ROI_MASK? I hope in your help. Thanks in advanced. Stefano ___ 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. ___ 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
[Freesurfer] dwi_orig.nii.gz does not exist
Hi list, I have a strange problem with TRACULA.The analysis run fine on all subjects but on the last two, -prep command produces this error: #@# Image corrections Mon Jul 20 09:09:54 CEST 2015mri_convert $SUBJECT/data.nii.gz $SUBJECT/dmri/dwi_orig.nii.gzcp $SUBJECT/bvecs.txt $SUBJECT/dmri/dwi_orig.mghdti.bvecscp $SUBJECT/bvals.txt $SUBJECT/dmri/dwi_orig.mghdti.bvalsmv -f $SUBJECT/dmri/bvecs.tmp $SUBJECT/dmri/dwi_orig.mghdti.bvecsmv -f $SUBJECT/dmri/bvals.tmp $SUBJECT/dmri/dwi_orig.mghdti.bvalsflip4fsl $SUBJECT/dmri/dwi_orig.nii.gz $SUBJECT/dmri/dwi_orig_flip.nii.gzERROR: $SUBJECT/dmri/dwi_orig.nii.gz does not exist and separatelly, mri_convert $SUBJECT/data.nii.gz $SUBJECT/dmri/dwi_orig.nii.gz did not produce any file. What's happened? Stefano ___ 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] Ubuntu 14.04 LTS 64 bits
Hi: Which freesurfer version must I install in Ubuntu 14.04 LTS 64 bits ?... Sincerely... Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Ubuntu 14.04 LTS 64 bits
The CentOS 6 x86_64 (64b) Platform release. Here is a link: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz -Zeke On 07/20/2015 10:10 AM, Gonzalo Rojas Costa wrote: Hi: Which freesurfer version must I install in Ubuntu 14.04 LTS 64 bits ?... Sincerely... Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.clc.cl ___ 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.
Re: [Freesurfer] Multimodal Extraction of Freesurfer ROI Intensity Values
Try mri_segstats. Run with --help for more info and examples doug On 07/17/2015 02:01 PM, Lakhani, Bimal wrote: Hello, To this point, I have been able to successfully register Myelin Water Fraction (MWF) scans to Freesurfer Base Space in the longitudinal pipeline (thank you for the help with that!). What I would like to do next is use Freesurfer ROIs to automatically extract the mean intensity of the MWF scans within each ROI. Is this possible using Freesurfer software or does this need to be done elsewhere. Ideally, I would like to be able to extract this information for all the ROIs that Freesurfer generates instead of individually extracting them, but I will take whatever is possible! Thanks again in advance. Best, Bimal *Bimal Lakhani, PhD| **Postdoctoral Fellow* Department of Physical Therapy *|*The University of British Columbia (604.827.3369 *|**_bimal.lakh...@ubc.ca mailto:bimal.lakh...@ubc.ca _*|***www.brain.rehab.med.ubc.ca http://www.brain.rehab.med.ubc.ca/ ___ 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.
Re: [Freesurfer] make_average_subject for subcortical volumes in children
Hi Kristi yes, that is correct. Everything is stored in native space and all processing is done there until you start doing group-level stuff cheers Bruce On Fri, 17 Jul 2015, Kristi Griffiths wrote: Dear FS experts, I am new to freesurfer and have a few basic questions. I have a sample of 8-17 year olds in which I will be looking at both cortical thickness and subcortical volumes. I understand that the surface-based registrations seem to be fine for this age range (as per Ghosh et al, 2010), but am wondering about the volume-based registrations? Should I be using make_average_subject to make a study specific target? Also, am I correct in thinking that the output from recon –all is in native space and that registration to common space only occurs at mris_preproc? Many thanks for any help! Best, Kristi ___ 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] R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity
On 07/20/2015 02:10 AM, std...@virgilio.it wrote: Hi list, in the previous mail you have suggested to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in $SUBJECTS_DIR/subject/mri). I have two question please. A- my mask is on vmPFC, thus it include the both hemispheres. Should I divide it in right and left? If yes, how can I do? You do not need to, just specify the appropriate index value. If they were divided between lh and rh and you wanted to merge them, you would just list the lh and rh indices. B- I have difficulties to run the fcseed-conf command: what do you mean by difficulties? fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.config fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config Is these command lines corrected? Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 13-lug-2015 10.16 A: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity Hi list, When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem to correspond. However, when I added the ROI_MASK.nii.gz, the orig is vanished, and is remained the ROI_MASK in correct position (and in white) and around all black. My concern is the correct binarization of ROI_MASK which it seem correct when I use fslview. fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs. After mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o func.vmPFC_MASK.nii The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with tkmedit and too big (a red bar which cover the whole) when I use fslview. With MRIcron, is screen is irregularly divided in half in black and white. Which should be the advised folder for func.vmPFC_MASK.nii? Thank you very much Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 30-giu-2015 0.36 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity Hi Stefano, sorry for the delay, I was traveling. It sounds like you just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask is in the orig.mgz space, then everything should work ok, but you can look at it with tkmedit -f orig.mgz -aux ROI_MASK.mgz You can also run mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o func.ROI_MASK.nii where template.nii.gz and register.dof6.dat are in the functional run folder doug On 06/12/2015 04:39 PM, std...@virgilio.it wrote: Hi list, I working on the combination of MRS and FS-FAST analysis. I have extracted the grey matter within voxel (I will call it ROI_MASK) by using FSL tools and now it is in the same space of orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I use fslview). I'd like to import it to FS for performing seed-based FS-FAST functional connectivity. The seed should the ROI MASK (GM within voxel). I know that the FSL and FS operate in different space and orientation. I think to have resolved the problem of different space by using orig.nii.gz to create ROI mask by FSL. However, I'm strongly worried for orientation issues. I have read the guidelines in FSL and FS sites, but I'm quite confused. In detail, I'd like to ask whether I should use mri_cor2label to transform ROI mask created by FSL to label. Furthmore, I'd like to be sure of the position of the ROI. How can I visualize it to be sure that the seed of my FS-FAST analysis is effectively the my ROI_MASK? I hope in your help. Thanks in advanced. Stefano ___ 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
Re: [Freesurfer] QDEC question
Does /home/anup/Desktop/QDEC/fsaverage/surf/lh.white exist? If not, cd /home/anup/Desktop/QDEC/ ln -s $FREESURFER_HOME/subjects fsaverage It looks like you will have a second problem in that the subject class GenderFemale-DiagnosisSCA1 does not have any members doug On 07/17/2015 08:17 AM, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do cortical thickness-age correlation in Spinocerebellar ataxia patients (SCA1 and SCA2). ## I successfully ran qcache command on these 10 subjects of SCA1 and SCA2. ##Since my discrete factors are *Gender *(Male and Female) and*Diagnosis* (SCA1 and SCA2), I created Gender.levels and Diagnosis.levels files as a superuser. ##My subject directory is /home/anup/Desktop/QDEC and the qdec.table.dat has this format: ID Gender Age Diagnosis l h-thickness AMARJEET Male 23 SCA1 2.45563 ANIL Male 25 SCA1 2.21909 ANNU Female 20 SCA2 2.36158 ASHOKSINGH Male 23 SCA2 2.41038 GANPAT Male 18 SCA2 2.30408 GOVIND Male 27 SCA1 2.32102 GULSAN Male 24 SCA2 2.36911 IMRAN Male 22 SCA2 2.31279 JASBIR Male 18 SCA2 2.3191 KAILASH Male 24 SCA1 2.36319 ##I copied the link of fsverage using the command on one of the thread of qdec for bash: if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi /So far, these all steps I have followed from freesurfer Qdec wiki.../ ##My subject directory which is /home/anup/Desktop/Qdec has all the 10 subjects, two .levels files, a qdec,table.dat file and link of fsaverage. After setting up the freesurfer and exporting the subject directory to I am able to load the qdec.table.dat file, which shows the following: Loading data table /home/anup/Desktop/QDEC/mydata.table.dat... Number of columns: 5 fsid column:1 Number of factors: 4 Number of subjects: 10 Reading discrete factor levels from config file /home/anup/Desktop/QDEC/Gender.levels Male Female done. Reading discrete factor levels from config file /home/anup/Desktop/QDEC/Diagnosis.levels SCA1 SCA2 done. ## I am also able to get the aparc and asegs data but when I click on the design tab which I named it as lh10 I get the following error: SUBJECTS_DIR : /home/anup/Desktop/QDEC Parsing the .stats files Building the table.. Writing the table to /home/anup/Desktop/QDEC/qdec/stats_tables//rh.aparc.a2009s.meancurv.stats.dat Completed creation of aseg and aparc stats data tables. lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000; lh-Avg-thickness-lh-thickness-Cor --- Does the correlation between thickness and lh-thickness, accounting for Gender and Diagnosis, differ from zero? 0.000 0.000 0.000 0.000 1.000 1.000 1.000 1.000; lh-Diff-Male-Female-Intercept-thickness --- Does the average thickness, accounting for Diagnosis, differ between Male and Female? 1.000 -1.000 1.000 -1.000 0.000 0.000 0.000 0.000; lh-Diff-Male-Female-Cor-thickness-lh-thickness --- Does the thickness--lh-thickness correlation, accounting for Diagnosis, differ between Male and Female? 0.000 0.000 0.000 0.000 1.000 -1.000 1.000 -1.000; lh-Diff-SCA1-SCA2-Intercept-thickness --- Does the average thickness, accounting for Gender, differ between SCA1 and SCA2? 1.000 1.000 -1.000 -1.000 0.000 0.000 0.000 0.000; lh-Diff-SCA1-SCA2-Cor-thickness-lh-thickness --- Does the thickness--lh-thickness correlation, accounting for Gender, differ between SCA1 and SCA2? 0.000 0.000 0.000 0.000 1.000 1.000 -1.000 -1.000; lh-X-Gender-Diagnosis-Intercept-thickness --- Is there a Gender--Diagnosis interaction in the mean thickness? 1.000 -1.000 -1.000 1.000 0.000 0.000 0.000 0.000; lh-X-Gender-Diagnosis-Cor-thickness-lh-thickness --- Is there a Gender--Diagnosis interaction in the thickness--lh-thickness correlation? 0.000 0.000 0.000 0.000 1.000 -1.000 -1.000 1.000; ninputs = 10 Checking inputs nframestot = 10 Allocing output Done allocing nframes = 10 Writing to /home/anup/Desktop/QDEC/qdec/lh-10/y.mgh gdfReadHeader: reading /home/anup/Desktop/QDEC/qdec/lh-10/qdec.fsgd WARNING: gdfReadV1: class GenderFemale-DiagnosisSCA1 is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 lh-thickness 2.3436 0.0612307 Class Means of each Continuous
Re: [Freesurfer] bad registration using mri_vol2vol
where did lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from? It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that transform to work On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote: Hello, I'm trying to convert an ROI mask I created in MNI305 space to MNI152. After running MRI_vol2vol the registration looks off (too anterior). Here are my commands: mri_convert -ot nii lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii mri_vol2vol --mov /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz --targ lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii --inv --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat --o new_lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii.gz Any ideas why the registration is off? Tracy ___ 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.
Re: [Freesurfer] error in atlas creation
Hello, I was wondering if these got uploaded correctly. Please let me know if I made a mistake and thanks, Anthony On 7/9/15 1:41 PM, Bruce Fischl wrote: sure On Thu, 9 Jul 2015, Anthony Dick wrote: Hello Bruce, I am still getting this error after re-running autorecon1 in the newest version of FS. Can I upload two brains and see what is the issue? I'm a bit stumped on this one. Anthony On 5/26/15 12:21 PM, Bruce Fischl wrote: Hi Anthony sorry, I know you've posted this before. What version are you running? And what type is your labeled data? That is, are they uchar? int? At some point this used to not work with non-uchar data, but I think I fixed it a while ago. YOu might try downloading a beta of V6 and see if it fixes your problem cheers Bruce On Tue, 26 May 2015, Anthony Dick wrote: Hello, I have been stumped by this error I keep getting using the rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, so I am wondering if the problem is with the brains we parcellated, or with my installation etc. The brains consist of manually segmented cerebellums from the original T1. The T1 is run through Freesurfer, and the ROIs are made in Freeview. The edited file is called seg_edited.mgz. Things run smoothly up until this error: using MR volume /path/subjects/4/mri/brain.mgz to mask input volume... reading 23 input volumes... logging results to talairach_one.log reading 'subjects/average/RB_one_2015-05-14.gca'... gcaAllocMax: node dims 32 32 32 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 8.4 using min determinant for regularization = 7.1 0 singular and 119 ill-conditioned covariance matrices regularized reading '/path/subjects/4/mri/nu.mgz'... reading '/path/subjects/average/RB_one_2015-05-14.gca'... gcaAllocMax: node dims 32 32 32 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading frame -1 of gca MRIcopyFrame: src and dst must be same type reading '/path/subjects/4/mri/transforms/talairach_one.lta'... mri_read(): couldn't determine type of file /path/subjects/4/mri/transforms/talairach_one.lta mri_em_register: could not open input volume /path/subjects/4/mri/transforms/talairach_one.lta. ___ 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: ad...@fiu.edu Webpage: faculty.fiu.edu/~adick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mac installation problems
When you tried recon-all again on subject bert, what was the error message? On 07/20/2015 12:02 PM, Austermuehle, Alison (NIH/NINDS) [F] wrote: Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When I tried to test the bert recon, I get this message: ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert When I do what the wiki suggests for admin issues (sudo chmod -R a+w $FREESURFER_HOME/subjects/bert),and try recon-all again, it quits with errors almost immediately. Note: I have full admin privileges on this computer. *My goal *is to take a folder with a long list of .dcm files and run a recon-all on it, which is currently on my desktop. Where does this folder need to be? Where is my subject directory? If someone with patience and generosity in their heart could help me out, using idiot-proof language, I would really appreciate it. Thanks, Alison Austermuehle NIH/NINDS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mac installation problems
As stated in the error message, you need to download a license file. This is required for all machines running freesurfer. Please follow the instructions under the License section of the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac -Zeke On 07/20/2015 12:20 PM, Austermuehle, Alison (NIH/NINDS) [F] wrote: Hi, Error as follows: ndsd-ces-5s205:mr_0007 austermuehleaa$ sudo chmod -R a+w $FREESURFER_HOME/subjects/bert ndsd-ces-5s205:mr_0007 austermuehleaa$ recon-all -s bert -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 root wheel 508990 Jul 20 09:58 /Applications/freesurfer/subjects/bert/scripts/recon-all.log Darwin ndsd-ces-5s205.ninds.nih.gov 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /space/freesurfer/centos4.0/stable # #@# MotionCor Mon Jul 20 11:38:04 EDT 2015 Found 3 runs /Applications/freesurfer/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/subjects/bert/mri/orig/002.mgz /Applications/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Applications/freesurfer/subjects/bert \n mri_robust_template --mov /Applications/freesurfer/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/subjects/bert/mri/orig/002.mgz /Applications/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /Applications/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Applications/freesurfer/subjects/bert/mri/orig/001-iscale.txt /Applications/freesurfer/subjects/bert/mri/orig/002-iscale.txt /Applications/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /Applications/freesurfer/subjects/bert/mri/orig/001.lta /Applications/freesurfer/subjects/bert/mri/orig/002.lta /Applications/freesurfer/subjects/bert/mri/orig/003.lta \n $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /Applications/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/Applications/freesurfer/subjects/bert/mri/orig/001.mgz'... -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Darwin ndsd-ces-5s205.ninds.nih.gov 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Mon Jul 20 11:38:06 EDT 2015 Alison Austermuehle NIH/NINDS (630) 267 1361 On 7/20/15, 12:18 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Hi Alison, what are your new errors (the ones you get almost immediately)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alison Austermuehle (NIH/NINDS) [F] alison.austermueh...@nih.gov To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 20, 2015 6:02:38 PM Subject: [Freesurfer] mac installation problems Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and
[Freesurfer] Correction with white-matter-points
Dear FreeSurfer Team! Last week I wrote about to the mailing list about problems occurring after the WM-point correction. Later I received a message in which You told me that You can help me if I upload the scan. Where and how can I do this? Thank You for Your help! Kind Regards Pawel W. Psychiatry and Neuroimaging Laboratory (PNL) Brigham and Women's Hospital Message: 6 Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction with white-matter-points To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.11.1507141133320.32...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Pawel does this happen in both versions? If so, upload a bad subject and we will take a look cheers Bruce On Tue, 14 Jul 2015, Wrobel, Pawel wrote: Dear FreeSurfer Team! We have a question concerning corrections with white-matter-points. We are currently working on a T1 data set. After performing Freesurfer-Segmentations several days ago, we corrected the intensity normalization in small regions (e.g. Gyrus temporalis superior) with WM-points, stricktly obeying the decription on the FreeSurfer-Website (wiki). Afterwards We used the following command: recon-all -autorecon2-cp -autorecon3 -subjid cp_before. The results in 80 % of corrections (105 scans) became worse than the first segmentation. In some cases the pial surface descends and sticks to the white matter surface, leaving the gray matter untouched, as if FreeSurfer would not recognize it. In some other cases the WM border touches the brain surface, including gray matter in the white matter. Sometimes the pial or white matter surface makes little incisions or loops into another compartment. We have been trying different approaches. We rerun the correction with an older FreeSurfer version (5.1.). We reinstalled the new version of FreeSurfer which we were using before (5.3). We tried it on different computers. We will be very thankful for Your help! Yours sincerely Pawel ___ 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] mac installation problems
Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When I tried to test the bert recon, I get this message: ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert When I do what the wiki suggests for admin issues (sudo chmod -R a+w $FREESURFER_HOME/subjects/bert),and try recon-all again, it quits with errors almost immediately. Note: I have full admin privileges on this computer. My goal is to take a folder with a long list of .dcm files and run a recon-all on it, which is currently on my desktop. Where does this folder need to be? Where is my subject directory? If someone with patience and generosity in their heart could help me out, using idiot-proof language, I would really appreciate it. Thanks, Alison Austermuehle NIH/NINDS ___ 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] Correction with white-matter-points
Hi Pawel you should look on the wiki for this type of info! Instructions are here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Mon, 20 Jul 2015, Wrobel, Pawel wrote: Dear FreeSurfer Team! Last week I wrote about to the mailing list about problems occurring after the WM-point correction. Later I received a message in which You told me that You can help me if I upload the scan. Where and how can I do this? Thank You for Your help! Kind Regards Pawel W. Psychiatry and Neuroimaging Laboratory (PNL) Brigham and Women's Hospital Message: 6 Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction with white-matter-points To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.11.1507141133320.32...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Pawel does this happen in both versions? If so, upload a bad subject and we will take a look cheers Bruce On Tue, 14 Jul 2015, Wrobel, Pawel wrote: Dear FreeSurfer Team! We have a question concerning corrections with white-matter-points. We are currently working on a T1 data set. After performing Freesurfer-Segmentations several days ago, we corrected the intensity normalization in small regions (e.g. Gyrus temporalis superior) with WM-points, stricktly obeying the decription on the FreeSurfer-Website (wiki). Afterwards We used the following command: recon-all -autorecon2-cp -autorecon3 -subjid cp_before. The results in 80 % of corrections (105 scans) became worse than the first segmentation. In some cases the pial surface descends and sticks to the white matter surface, leaving the gray matter untouched, as if FreeSurfer would not recognize it. In some other cases the WM border touches the brain surface, including gray matter in the white matter. Sometimes the pial or white matter surface makes little incisions or loops into another compartment. We have been trying different approaches. We rerun the correction with an older FreeSurfer version (5.1.). We reinstalled the new version of FreeSurfer which we were using before (5.3). We tried it on different computers. We will be very thankful for Your help! Yours sincerely Pawel ___ 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.
Re: [Freesurfer] mac installation problems
Hi, Error as follows: ndsd-ces-5s205:mr_0007 austermuehleaa$ sudo chmod -R a+w $FREESURFER_HOME/subjects/bert ndsd-ces-5s205:mr_0007 austermuehleaa$ recon-all -s bert -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 root wheel 508990 Jul 20 09:58 /Applications/freesurfer/subjects/bert/scripts/recon-all.log Darwin ndsd-ces-5s205.ninds.nih.gov 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /space/freesurfer/centos4.0/stable # #@# MotionCor Mon Jul 20 11:38:04 EDT 2015 Found 3 runs /Applications/freesurfer/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/subjects/bert/mri/orig/002.mgz /Applications/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Applications/freesurfer/subjects/bert \n mri_robust_template --mov /Applications/freesurfer/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/subjects/bert/mri/orig/002.mgz /Applications/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /Applications/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Applications/freesurfer/subjects/bert/mri/orig/001-iscale.txt /Applications/freesurfer/subjects/bert/mri/orig/002-iscale.txt /Applications/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /Applications/freesurfer/subjects/bert/mri/orig/001.lta /Applications/freesurfer/subjects/bert/mri/orig/002.lta /Applications/freesurfer/subjects/bert/mri/orig/003.lta \n $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /Applications/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/Applications/freesurfer/subjects/bert/mri/orig/001.mgz'... -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Darwin ndsd-ces-5s205.ninds.nih.gov 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Mon Jul 20 11:38:06 EDT 2015 Alison Austermuehle NIH/NINDS (630) 267 1361 On 7/20/15, 12:18 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Hi Alison, what are your new errors (the ones you get almost immediately)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alison Austermuehle (NIH/NINDS) [F] alison.austermueh...@nih.gov To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 20, 2015 6:02:38 PM Subject: [Freesurfer] mac installation problems Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When I tried to test the bert recon, I get this message: ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert When I do what the wiki suggests for admin issues ( sudo chmod -R a+w $FREESURFER_HOME/subjects/bert) , and try recon-all again, it quits with errors almost immediately. Note: I have full admin privileges on this computer.
Re: [Freesurfer] mac installation problems
ndsd-ces-5s205:mr_0007 austermuehleaa$ sudo chmod -R a+w $FREESURFER_HOME/subjects/bert ndsd-ces-5s205:mr_0007 austermuehleaa$ recon-all -s bert -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 root wheel 508990 Jul 20 09:58 /Applications/freesurfer/subjects/bert/scripts/recon-all.log Darwin ndsd-ces-5s205.ninds.nih.gov 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /space/freesurfer/centos4.0/stable # #@# MotionCor Mon Jul 20 11:38:04 EDT 2015 Found 3 runs /Applications/freesurfer/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/subjects/bert/mri/orig/002.mgz /Applications/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #--- /Applications/freesurfer/subjects/bert \n mri_robust_template --mov /Applications/freesurfer/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/subjects/bert/mri/orig/002.mgz /Applications/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /Applications/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Applications/freesurfer/subjects/bert/mri/orig/001-iscale.txt /Applications/freesurfer/subjects/bert/mri/orig/002-iscale.txt /Applications/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /Applications/freesurfer/subjects/bert/mri/orig/001.lta /Applications/freesurfer/subjects/bert/mri/orig/002.lta /Applications/freesurfer/subjects/bert/mri/orig/003.lta \n $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /Applications/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/Applications/freesurfer/subjects/bert/mri/orig/001.mgz'... -- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Darwin ndsd-ces-5s205.ninds.nih.gov 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Mon Jul 20 11:38:06 EDT 2015 Alison Austermuehle NIH/NINDS (630) 267 1361 On 7/20/15, 12:16 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: When you tried recon-all again on subject bert, what was the error message? On 07/20/2015 12:02 PM, Austermuehle, Alison (NIH/NINDS) [F] wrote: Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When I tried to test the bert recon, I get this message: ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert When I do what the wiki suggests for admin issues (sudo chmod -R a+w $FREESURFER_HOME/subjects/bert),and try recon-all again, it quits with errors almost immediately. Note: I have full admin privileges on this computer. *My goal *is to take a folder with a long list of .dcm files and run a recon-all on it, which is currently on my desktop. Where does this folder need to be? Where is my subject directory? If someone with patience and generosity in their heart could help me out, using idiot-proof language, I would really appreciate it. Thanks, Alison
Re: [Freesurfer] mac installation problems
Hi Alison, what are your new errors (the ones you get almost immediately)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alison Austermuehle (NIH/NINDS) [F] alison.austermueh...@nih.gov To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 20, 2015 6:02:38 PM Subject: [Freesurfer] mac installation problems Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When I tried to test the bert recon, I get this message: ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert When I do what the wiki suggests for admin issues ( sudo chmod -R a+w $FREESURFER_HOME/subjects/bert) , and try recon-all again, it quits with errors almost immediately. Note: I have full admin privileges on this computer. My goal is to take a folder with a long list of .dcm files and run a recon-all on it, which is currently on my desktop. Where does this folder need to be? Where is my subject directory? If someone with patience and generosity in their heart could help me out, using idiot-proof language, I would really appreciate it. Thanks, Alison Austermuehle NIH/NINDS ___ 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_label2vol change to MNI 152
Hi Freesurfer listserve, I hope you are well. I emailed the freesurfer listserve also but got no response. I am trying to take an functional ROI that is anatomically constrined that I created using tkmedit and transform it to MNI152 space. I saved it as $label.label. Then did this command: mri_label2vol --subject fsaverage --label /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label --o $TARGET_DIR/tracy_$label.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --temp /usr/pubsw/packages/fsl/4.1.4/data/standard/MNI152_T1_2mm.nii.gz. When I look at the new ROI in FSL view it looks a bit off (now more in the hippocampus than the amygdala). Is there a step that I missed or is there something wrong with this command line? Thank you in advance! Tracy ___ 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] help with using optseq2
The problem is probably that you have specified a maximum for the null event and it just does not need as much run time (# of time points) that you have allocated. On 07/16/2015 06:17 PM, Heeyoung Choo wrote: Hello, I'm trying to create trial sequences for a slow event related fMRI experiment. I have 10 classes of stimuli, and each stimulus lasts 5 sec and repeats twice in a run. Environment: Linux 3.13.0-35-generic #62-Ubuntu SMP UTC 2014 x86_64 x86_64 x86_64 GNU/Linux I ran: ./optseq2 --ntp 144 --tr 2.5 \ --ev evt1 5 2 --ev evt2 5 2 --ev evt3 5 2 --ev evt4 5 2 --ev evt5 5 2 --ev evt6 5 2 --ev evt7 5 2 --ev evt8 5 2 --ev evt9 5 2 --ev evt10 5 2 \ --nkeep 10 --psdwin 0 20 --o exp_video \ --tnullmax 25 --tnullmin 7.5 \ --nsearch 1 Almost all of the sequences have extremely long NULL at the end of a run, like 82.5sec (please see one of sequences below). I am aware that optseq2 is for rapid event related fMRI, and wonder if the problem is due to specific parameters of my design, or due to a bug. I would appreciate any comments or help. Thank you very much! Best regards, Heeyoung 0.55.000 1. evt5 5.07.500 1. NULL 12.500095.000 1. evt9 17.500007.500 1. NULL 25.35.000 1. evt3 30.07.500 1. NULL 37.5000 105.000 1. evt10 42.50000 12.500 1. NULL 55.75.000 1. evt7 60.0 10.000 1. NULL 70.35.000 1. evt3 75.07.500 1. NULL 82.500045.000 1. evt4 87.50000 15.000 1. NULL 102.500065.000 1. evt6 107.500007.500 1. NULL 115.65.000 1. evt6 120.0 10.000 1. NULL 130.85.000 1. evt8 135.0 17.500 1. NULL 152.500015.000 1. evt1 157.500007.500 1. NULL 165.25.000 1. evt2 170.07.500 1. NULL 177.5000 105.000 1. evt10 182.500007.500 1. NULL 190.85.000 1. evt8 195.07.500 1. NULL 202.500095.000 1. evt9 207.50000 12.500 1. NULL 220.45.000 1. evt4 225.07.500 1. NULL 232.500075.000 1. evt7 237.500007.500 1. NULL 245.15.000 1. evt1 250.07.500 1. NULL 257.500055.000 1. evt5 262.50000 10.000 1. NULL 272.500025.000 1. evt2 277.50000 82.500 1. NULL ___ 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.
Re: [Freesurfer] help on mris_preproc
I think you have a non-standard directory structure. FS is expecting something like $SUBJECTS_DIR/subject1 but it looks like you have the FS results in $SUBJECTS_DIR/subject1/freesurfer You have to use the FS structure or else it will generate an error doug On 07/20/2015 03:14 PM, David C. Zhu wrote: Dear Doug, I was away a while and missed your email. I have not resolved this issue yet. Could you please help? Thanks. David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, June 29, 2015 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help on mris_preproc Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: Hi Doug, Thanks. I can see that the mris_preproc command reads the header information in register.dat. I set the . as the $SUBJECTS_DIR, and thus it seems that mris_preproc cannot locate the path. Is there a way to fix this? David Here is the (part of) output: -- end while ( $#argv != 0 ) while ( 27 != 0 ) set flag = $argv[1] ; shift ; set flag = --iv shift switch ( $flag ) switch ( --iv ) case --ivp: case --ivp: if ( $#argv 2 ) goto arg2err ; if ( 26 2 ) goto arg2err set ivp = $argv[1] ; shift ; set ivp = S02520110927_Free/sum_all_norm_IRF_EA.nii shift if ( ! -e $ivp ) then if ( ! -e S02520110927_Free/sum_all_norm_IRF_EA.nii ) then set irp = $argv[1] ; shift ; set irp = S02520110927_Free/register.dat shift if ( ! -e $irp ) then if ( ! -e S02520110927_Free/register.dat ) then set ivplist = ( $ivplist $ivp ) ; set ivplist = ( S00720110927_Free/sum_all_norm_IRF_EA.nii S01420110908_Free/sum_all_norm_IRF_EA.nii S01520110811_Free/sum_all_norm_IRF_EA.nii S02520110927_Free/sum_all_norm_IRF_EA.nii ) set irplist = ( $irplist $irp ) ; set irplist = ( S00720110927_Free/register.dat S01420110908_Free/register.dat S01520110811_Free/register.dat S02520110927_Free/register.dat ) set subj = `head -1 $irp` ; set subj = `head -1 $irp` head -1 S02520110927_Free/register.dat set subjlist = ( $subjlist $subj ) ; set subjlist = ( freesurfer freesurfer freesurfer freesurfer ) set srcvol = 1 ; set srcvol = 1 breaksw breaksw end end ... ... ... if ( 0 == 0 1 == 0 0 == 0 ) then if ( $srcsurf $srcvol ) then if ( 0 1 ) then if ( $srcsurf $#projfrac != 0 ) then if ( 0 0 != 0 ) then if ( $catmean $catstd ) then if ( 0 0 ) then if ( $#meas $#isplist ) then if ( 0 0 ) then if ( $MeasIn $CacheIn ) then if ( 0 0 ) then if ( $#ivplist != 0 ) then if ( 12 != 0 ) then if ( $#ivplist != $#subjlist ) then if ( 12 != 12 ) then endif endif if ( $#isplist != 0 ) then if ( 0 != 0 ) then if ( $paireddiff ! $DoXHemi ) then if ( 0 ! 0 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e . ) then if ( $DoXHemi ) then if ( 0 ) then echo nsubjects = $#subjlist ; echo nsubjects = 12 nsubjects = 12 @ nthsubj = 1 ; @ nthsubj = 1 foreach subj ( $subjlist ) foreach subj ( freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer ) set subjpath = $SUBJECTS_DIR/$subj set subjpath = ./freesurfer if ( ! -e $subjpath ) then if ( ! -e ./freesurfer ) then echo ERROR: cannot find $subjpath echo ERROR: cannot find ./freesurfer ERROR: cannot find ./freesurfer exit 1 ; exit 1 *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Friday, June 12, 2015 3:51 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] help on mris_preproc Can you run the 2nd command with --debug as the first option and send the terminal output? doug On 6/12/15 12:09 PM, David C. Zhu wrote: Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric analyses. I want to give a try to use it for surface-based fMRI analyses. I encountered some issues with mris_preproc to assemble IRF results to the fsaverage surface. Please advise on how to resolve these issues. Here is what I did: After finishing recon-all on each subject, I ran this following on each subject. bbregister --mov reg_cat_TSall_before_blur.nii --bold --s freesurfer --init-fsl --lta register.lta reg_cat_TSall_before_blur.nii is the EPI fMRI time series assembled together. Then I calculated the IRF percent signal changes for different conditions. sum_all_norm_IRF_EA.nii is for one condition. Now I want to assemble the sum_all_norm_IRF_EA.nii from each subject and put them on the fsaverage surface. I got the following errors: mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \ --iv S00720110927_Free/sum_all_norm_IRF_EA.nii S00720110927_Free/register.lta \
Re: [Freesurfer] help on mris_preproc
Dear Doug, I was away a while and missed your email. I have not resolved this issue yet. Could you please help? Thanks. David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, June 29, 2015 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help on mris_preproc Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: Hi Doug, Thanks. I can see that the mris_preproc command reads the header information in register.dat. I set the . as the $SUBJECTS_DIR, and thus it seems that mris_preproc cannot locate the path. Is there a way to fix this? David Here is the (part of) output: -- end while ( $#argv != 0 ) while ( 27 != 0 ) set flag = $argv[1] ; shift ; set flag = --iv shift switch ( $flag ) switch ( --iv ) case --ivp: case --ivp: if ( $#argv 2 ) goto arg2err ; if ( 26 2 ) goto arg2err set ivp = $argv[1] ; shift ; set ivp = S02520110927_Free/sum_all_norm_IRF_EA.nii shift if ( ! -e $ivp ) then if ( ! -e S02520110927_Free/sum_all_norm_IRF_EA.nii ) then set irp = $argv[1] ; shift ; set irp = S02520110927_Free/register.dat shift if ( ! -e $irp ) then if ( ! -e S02520110927_Free/register.dat ) then set ivplist = ( $ivplist $ivp ) ; set ivplist = ( S00720110927_Free/sum_all_norm_IRF_EA.nii S01420110908_Free/sum_all_norm_IRF_EA.nii S01520110811_Free/sum_all_norm_IRF_EA.nii S02520110927_Free/sum_all_norm_IRF_EA.nii ) set irplist = ( $irplist $irp ) ; set irplist = ( S00720110927_Free/register.dat S01420110908_Free/register.dat S01520110811_Free/register.dat S02520110927_Free/register.dat ) set subj = `head -1 $irp` ; set subj = `head -1 $irp` head -1 S02520110927_Free/register.dat set subjlist = ( $subjlist $subj ) ; set subjlist = ( freesurfer freesurfer freesurfer freesurfer ) set srcvol = 1 ; set srcvol = 1 breaksw breaksw end end ... ... ... if ( 0 == 0 1 == 0 0 == 0 ) then if ( $srcsurf $srcvol ) then if ( 0 1 ) then if ( $srcsurf $#projfrac != 0 ) then if ( 0 0 != 0 ) then if ( $catmean $catstd ) then if ( 0 0 ) then if ( $#meas $#isplist ) then if ( 0 0 ) then if ( $MeasIn $CacheIn ) then if ( 0 0 ) then if ( $#ivplist != 0 ) then if ( 12 != 0 ) then if ( $#ivplist != $#subjlist ) then if ( 12 != 12 ) then endif endif if ( $#isplist != 0 ) then if ( 0 != 0 ) then if ( $paireddiff ! $DoXHemi ) then if ( 0 ! 0 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e . ) then if ( $DoXHemi ) then if ( 0 ) then echo nsubjects = $#subjlist ; echo nsubjects = 12 nsubjects = 12 @ nthsubj = 1 ; @ nthsubj = 1 foreach subj ( $subjlist ) foreach subj ( freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer ) set subjpath = $SUBJECTS_DIR/$subj set subjpath = ./freesurfer if ( ! -e $subjpath ) then if ( ! -e ./freesurfer ) then echo ERROR: cannot find $subjpath echo ERROR: cannot find ./freesurfer ERROR: cannot find ./freesurfer exit 1 ; exit 1 *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Friday, June 12, 2015 3:51 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] help on mris_preproc Can you run the 2nd command with --debug as the first option and send the terminal output? doug On 6/12/15 12:09 PM, David C. Zhu wrote: Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric analyses. I want to give a try to use it for surface-based fMRI analyses. I encountered some issues with mris_preproc to assemble IRF results to the fsaverage surface. Please advise on how to resolve these issues. Here is what I did: After finishing recon-all on each subject, I ran this following on each subject. bbregister --mov reg_cat_TSall_before_blur.nii --bold --s freesurfer --init-fsl --lta register.lta reg_cat_TSall_before_blur.nii is the EPI fMRI time series assembled together. Then I calculated the IRF percent signal changes for different conditions. sum_all_norm_IRF_EA.nii is for one condition. Now I want to assemble the sum_all_norm_IRF_EA.nii from each subject and put them on the fsaverage surface. I got the following errors: mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \ --iv S00720110927_Free/sum_all_norm_IRF_EA.nii S00720110927_Free/register.lta \ --iv S01420110908_Free/sum_all_norm_IRF_EA.nii S01420110908_Free/register.lta \ --iv S01520110811_Free/sum_all_norm_IRF_EA.nii S01520110811_Free/register.lta \ --iv S02520110927_Free/sum_all_norm_IRF_EA.nii S02520110927_Free/register.lta \ --iv
[Freesurfer] Dividing Entire Scan By Intensity Factor Create Overlay Surface
Hello again and thank you for the continual help! As before, I am continuing down the path of registering/extracting data from Myelin Water Fraction Scans using the outputs from the Freesurfer Longitudinal Pipeline. As the intensity is the main outcome measure of the MWF, I would like to display that directly and without scaling. When completing the mri_robust_register, however, I have to use the —iscale option because the intensity of the —mov and —dst files are extremely different and registration fails without this option. I am currently exporting the scale factor using —iscaleout. This is useful to get the extracted data back into usable units, but I was wondering if there is anyway to ‘divide' the entire scan by this factor so that when visualizing the data, the scale is accurate and appropriate for the data I am presenting. The second part of this question has to do specifically with that visualization. I would like to create an overlay to project on an inflated hemisphere file but am having a bit of trouble with this. Here is the code I am using mri_vol2surf —src J01_MWF2Brain.mgz —srcreg J01_MWF2Brain.dat —out J01_MWF_surf.mgz —out_type mgz —hemi lh —projfrac 0.5 This does generate an output that I am able to overlay, however it does not appear to be the right size (lots of clipping) and just generally doesn’t look correct. Just a note that if I overlay the original J01_MWF2Brain.mgz file on the pial surface, it looks quite good, so it looks like something is going wrong in the mri_vol2surf section. Thanks very much as always, Bimal ___ 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.
