[Freesurfer] mris_convert
Hi Freesurfer experts, I am trying to run tracktography from freesurfer labels using probtrackx2 in fsl. To convert the labels to surfaces I use the label2surf command as recommended on the fslwiki. To use the label2surf command I need to convert the surface, e.g. lh.white into a fsl-compatible format using mris_convert: mris_convert lh.white lh.white.gii When I load lh.white and the created lh.white.gii into freeview the two are not aligned. Aren't they suppose to be similar when lh.white.gii is use in the label2surf command? Do I need additional arguments in the mris_convert command? Best, Karen ___ 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] longitudinal process
Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna ___ 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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu ___ 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] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]
Hi all When you loaded the lowb into freeview and it looked registered with the anatomical, did you load the lowb with the registration file? If not, then the registration may be wrong. Things may look almost right when you don't specify a registration file because you probably collected the dti and anatomical in the same session. If so, then check the registration with something like tkregister2 --mov lowb.nii.gz --reg anatorig2diff.bbr.dat --surfs I did not load it with the registration file, but I just did and it does not change the results on freeview. I also checked the registration on tkregister and it seems very fine to me. also, what is the first value in anatorig2diff.bbr.dat.mincost? Here are all the values: 0.180949 209.653007 285.934948 29.944402 Maybe one point that I don't understand is why we have to apply a registration matrix if all the volumes (brainmask.mgz, lowb.nii.gz and the lesion mask) are already registered? Because if I am applying the invert of registration matrix anatorig2diff.bbr.dat to the lesion mask, then it will be in the native diffusion space, not the recons space anymore, isn't it? doug On 2/17/14 10:41 PM, Celine Louapre wrote: The lesion_vol2vol volume is still not correctly overlapping the DTI. The only command that didn't give me registration issue is mri_convert where I did not put any registration file but I was not completely happy with the interpolation resampling. (nearest missed some lesions, maybe interpolate and then binarize the mask was one possible option). I can show you the results tomorrow if you prefer Celine what does it look like if you run tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1 On 2/17/14 10:00 PM, Celine Louapre wrote: No problem, sorry! So when I am loading my lesion mask on freeview on brainmask.mgz and on DTI_fit_FA.nii, the lesions are correctly registered on both DTI and T1. The only thing I would like to do is to resample the lesion mask that has a resolution of 0.3*0.3*1 on the resolution of the DTI that has 1.8mm^3. When I am using the command below with mri_vol2vol, and the registration matrix anatorig2diff.bbr.dat, the output is a lesion mask that has 1.8mm3 resolution, but the lesions are not overlapping the other modalities and the previous mask on freeview. Is it the way I am loading it on freeview maybe? or actually all the volumes are already on the recons space so maybe I should not use any registration matrix? Celine oops, sorry! That command looks like it is correct. Can you say more about what is going wrong? How are you determining that something is going wrong? doug On 2/17/14 9:30 PM, Celine Louapre wrote: Hi Doug I don't know if you had the chance to read my email below to resample a lesion mask on diffusion images. Anastasia gave me the registration file to use (anatorig2diff.bbr.dat) in the command but the output mask file was not registered anymore. So she asked me to rephrase my question more generally on the mailing list to look for help with bbregister. Thanks a lot Celine Original Message Subject: [Freesurfer] Resample a mask on diffusion images using bbregister registration matrix From:Celine Louapre cel...@nmr.mgh.harvard.edu Date:Thu, February 13, 2014 9:58 pm To: freesurfer@nmr.mgh.harvard.edu -- Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images to further exclude the lesion voxels on the DTI maps (and to calculate DTI metrics within the lesions too). Using mri_vol2vol command I think I am missing something because I tried with the registration file produced by bbregister (through tracula) but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seems correctly registered on both. The command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size is the same as the DTI images, but the lesions are not at the same place. On the mailing list I have also seen other options but I am not sure if they would be appropriate? I have seen mri_label2vol command where I could set the fill threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot
[Freesurfer] fReadQdec question
Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin___ 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] fReadQdec question
yes, it has a certain format. Look at the examples on the wiki doug On 02/18/2014 11:19 AM, sabin khadka wrote: Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin ___ 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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ ___ 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] Which is broken - GCC or Freesurfer build?
This GLIBCXX error appears when running our Centos 6 build on an older OS. Try using our Centos 4 build. Nick On Mon, 2014-02-17 at 09:32 -0500, Bruce Fischl wrote: yes, it certainly looks like a library problem. You should talk to your sysadmin, or perhaps Zeke or Nick can comment cheers Bruce On Mon, 17 Feb 2014, Durai Arasan wrote: Hi Freesurfer experts, so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. Thank you *** *** Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /** Actual FREESURFER_HOME /** Linux * SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl) tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar) mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize) mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed) mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut) mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment) mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label) mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register) mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize) mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_normalize) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_register) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_register) mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_register) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_label) mri_ca_label:
Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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 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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
It will tend to weight smaller groups by a proportion greater than the number of subjects in the group. On 02/18/2014 01:58 PM, Yang, Daniel wrote: Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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. -- 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
Re: [Freesurfer] BVECS and BVALS file
That helps a lot. Thanks Anastasia: best, Alan On Mon, Feb 17, 2014 at 11:04 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - If you're using a standard MGH diffusion sequence and you have a Martinos account, look for the appropriate gradient table in this directory: $FREESURFER_HOME/diffusion/mgh-dti-seqpack/ You'll have to find out how many gradient directions are in your data (that's the number of frames in your nifti file, minus the number of frames that are b=0 images), and then get the corresponding file from the directory above. Hope this helps, a.y On Mon, 17 Feb 2014, Alan Francis wrote: Hi Anastasia: Yes I am using a standard MGH diffusion sequence. thanks, Alan On Fri, Feb 14, 2014 at 10:20 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - The gradient table is not saved in the nifti header. Are you using a standard MGH diffusion sequence? a.y On Fri, 14 Feb 2014, Alan Francis wrote: Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header on MRICRON but how does one convert these values into table form. thanks so much, Alan Martinos Center. 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 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] longitudinal process
Hi Anna, the linear mixed effects models can include subjects with a single time point and it would be a shame to drop that information. That is why we modified the longitudinal pipeline (use 5.3) to allow processing of subjects with a single time point. However, it is necessary that these images undergo the same processing steps as the rest of the data (to avoid bias). So you run it exactly as other subjects, with a cross sectional, -base and a -long step: recon-all -all -s tp1id -i path_to_tp1_dcm recon-all -base templateid -tp tp1id -all recon-all -long tp1id templateid -all Best, Martin On 02/18/2014 04:58 AM, Anna Jonsson wrote: Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] fReadQdec question
Hi Doug, Thanks for the reply. Yeah I have my qdec.table.dat file in the same format as wiki says and in tab delimited format. But when I try to run fReadQdec it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I was assuming it would give me N X M(no of columns for each variable that I put in table). -Sabin On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, it has a certain format. Look at the examples on the wiki doug On 02/18/2014 11:19 AM, sabin khadka wrote: Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin ___ 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 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] fReadQdec question
where did you get this m file from? I don't see it in our distribution. On 02/18/2014 03:29 PM, sabin khadka wrote: Hi Doug, Thanks for the reply. Yeah I have my qdec.table.dat file in the same format as wiki says and in tab delimited format. But when I try to run fReadQdec it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I was assuming it would give me N X M(no of columns for each variable that I put in table). -Sabin On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, it has a certain format. Look at the examples on the wiki doug On 02/18/2014 11:19 AM, sabin khadka wrote: Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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. -- 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
Re: [Freesurfer] fReadQdec question
Its under freesurfer/matlab/lme/Qdec. This is what is suggested to use while performing linear mixed effects models in freesurfer. http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels On Tuesday, February 18, 2014 3:35 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: where did you get this m file from? I don't see it in our distribution. On 02/18/2014 03:29 PM, sabin khadka wrote: Hi Doug, Thanks for the reply. Yeah I have my qdec.table.dat file in the same format as wiki says and in tab delimited format. But when I try to run fReadQdec it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I was assuming it would give me N X M(no of columns for each variable that I put in table). -Sabin On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, it has a certain format. Look at the examples on the wiki doug On 02/18/2014 11:19 AM, sabin khadka wrote: Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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. -- 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___ 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] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Doug, sorry, I am not sure I can fully understand. Do you mean the results are weighted MORE toward groups with smaller sample sizes (than groups with larger sample sizes)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/18/14 2:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It will tend to weight smaller groups by a proportion greater than the number of subjects in the group. On 02/18/2014 01:58 PM, Yang, Daniel wrote: Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.edumailto:gr...@nmr.mgh.harvard.edu mailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor
Let's say you have four groups with 10 20 30 40 (100 total). The first group would get a weight of .25 where it only had 10% of the total. I don't think there is any way around this. On 2/18/14 4:07 PM, Yang, Daniel wrote: Doug, sorry, I am not sure I can fully understand. Do you mean the results are weighted MORE toward groups with smaller sample sizes (than groups with larger sample sizes)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ On 2/18/14 2:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It will tend to weight smaller groups by a proportion greater than the number of subjects in the group. On 02/18/2014 01:58 PM, Yang, Daniel wrote: Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would the effect be biased toward large sample sizes in one of the groups (versus the other groups)? Or, does FreeSurfer qdec take care of the unequal cell, in a possible way analogous to using Type III SS in the traditional ANOVA? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ On 2/18/14 1:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E wrote: That looks right to me doug On 02/18/2014 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer experts, I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), and 1 nuisance factor (NUI). I want to make sense of some specification of the regressors and contrasts. Because they are not described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding below. Can you let me know if it is correct? This model using the DODS method will have 12 regressors: Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1) Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2) Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3) Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4) Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1) Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2) Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3) Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4) Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1) Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2) Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3) Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4) Description1: Does the correlation between thickness and COV, accounting for F1 and F2, differ from 0? Nuisance factors: NUI Contrast1: [0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0] Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: _yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center
Re: [Freesurfer] problems with control points
Thanks SO much! I'll let you know if I have further problems. Thanks again. Best, Pietro Inviato da iPhone Il giorno 18/feb/2014, alle ore 16:38, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu ha scritto: Hi Pietro, There were some disconnected pieces of wm on the wm.mgz which was presumably causing a poor wm surf initialization and further problems downstream. Filling in the gaps on several slices seems to have done the trick. Snapshot attached. -Louis On Thu, 13 Feb 2014, pietro de rossi wrote: Dear FreeSurfers, I have uploaded a subject I am trying to edit by using control points. Control points worked in most of the regions that needed to be editedwith the exception of right superior temporal gyrus. I tried to put control points there and re-running -autorecon2-cp -autorecon-3 several times but it didn't work... Could you please have a look? Any suggestion would be greatly appreciated :-) Thanks in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com 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. wm_fill.JPEG ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error mric-convert
Hello Everyone, I am facing small problem to create my own file //// saurabh@saurabh-Precision-WorkStation-T3500:~/Desktop/saurabh_freesurfer/bert/sam$ mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o $SUBJECTS_DIR/bert/mri/orig/005.mgz mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/005.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001... Starting DICOMRead2() dcmfile = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 dcmdir = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam Ref Series No = 501 *Found 156 files, checking for dicoms WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154* Found 151 dicom files in series. WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 First Sorting Computing Slice Direction Vs: -121.791 -125.08 -36.7045 Vs: -0.682698 -0.701136 -0.205747 Second Sorting Counting frames nframes = 1 nslices = 151 *ndcmfiles = 151 MRIalloc(0, 0, 151): bad parmNo such file or directoryERROR: mri alloc failed* //===// Please reply asapi m waiting for the solution. Thanks in advanced. cheers Saurabh Thakur, ___ 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 mric-convert
command i m using is :mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o $SUBJECTS_DIR/bert/mri/orig/005.mgz cheers Saurabh Thakur, On Wed, Feb 19, 2014 at 12:22 PM, Saurabh Thakur srbht...@gmail.com wrote: Hello Everyone, I am facing small problem to create my own file //// saurabh@saurabh-Precision-WorkStation-T3500:~/Desktop/saurabh_freesurfer/bert/sam$ mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o $SUBJECTS_DIR/bert/mri/orig/005.mgz mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/005.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001... Starting DICOMRead2() dcmfile = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 dcmdir = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam Ref Series No = 501 *Found 156 files, checking for dicoms WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154* Found 151 dicom files in series. WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 First Sorting Computing Slice Direction Vs: -121.791 -125.08 -36.7045 Vs: -0.682698 -0.701136 -0.205747 Second Sorting Counting frames nframes = 1 nslices = 151 *ndcmfiles = 151 MRIalloc(0, 0, 151): bad parmNo such file or directoryERROR: mri alloc failed* //===// Please reply asapi m waiting for the solution. Thanks in advanced. cheers Saurabh Thakur, ___ 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.
