Hi Mohamed, please remember to post to the list. As for your question, what aparc files are you looking at? Those measures are in, eg, lh.aparc.stats
On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote:
Dear Douglas,
Many thanks for your answer!
We are interested on one region belonging to the Brodmann areas "Perirhinal". Cortical thickness as well as volume values appear on the BA stat list and not on the aparc or aseg lists. Does the ROI-based analysis could be used for this BA region?
Best regards,
Mohamed
On 05/11/2017 18:46, Douglas Greve wrote:
Do you just want to do an ROI analysis? Or do you want to do a voxel-based analysis? If ROI-based, then follow the steps on the ROI tutorial (ie, aparcstats2table and mri_glmfit with --table input).
On 11/3/17 4:08 PM, Bruce Fischl wrote:
Hi Mohamed
Doug is away this week and can give you a more details answer next week. Certainly you could use mris_anatomical_stats -l <BA label file name> to compute the volume/thickness/area for each subject then do whatever GLM analysis you want outside of FS.
cheers Bruce
On Fri, 3 Nov 2017, m.bahri@uliege.be wrote:
Dear All, Does anyone have an answer to the following VBM question?
Many thanks in advance, Regards
-----Mail original----- De: "Mohamed Ali Bahri" m.bahri@uliege.be À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM Objet: [Freesurfer] VBM question
Dear Freesurfer users,
I would like to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. I tried to do that with Qdec tool but unfortunately Qdec does not load the Brodmann areas stat list. I am wondering if I could use the GLM formalism with of course regressing out the ITV. Any suggestion/advice will be very welcome.
Many thanks in advance,
Best regards,
Mohamed
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.
-- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri@uliege.be
Dear Douglas,
Thank you very much for you answer. I checked all the aparc stat files (/Freesurfer/subjects/subjectID/stats/lh.aparc.stats; lh.aparc.a2009s.stats ....) and my region of interest "perirhinal" (region extending on BA35 and BA36 areas) is only present on the lh/rh.BA.stats files (/Freesurfer/subjects/subjectID/stats/lh.BA.stats and rh.BA.stats). I use Freesurfer version 5.3. When using Qdec tool the only uploadable files are .aparc files. Is it possible to upload also the regions of BA.stats files?
Best regards, Mohamed
----- Mail original ----- De: "Douglas N Greve" greve@nmr.mgh.harvard.edu À: "Mohamed Ali Bahri" m.bahri@uliege.be, freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 6 Novembre 2017 23:44:43 Objet: Re: [Freesurfer] Trans. : VBM question
Hi Mohamed, please remember to post to the list. As for your question, what aparc files are you looking at? Those measures are in, eg, lh.aparc.stats
On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote:
Dear Douglas,
Many thanks for your answer!
We are interested on one region belonging to the Brodmann areas "Perirhinal". Cortical thickness as well as volume values appear on the BA stat list and not on the aparc or aseg lists. Does the ROI-based analysis could be used for this BA region?
Best regards,
Mohamed
On 05/11/2017 18:46, Douglas Greve wrote:
Do you just want to do an ROI analysis? Or do you want to do a voxel-based analysis? If ROI-based, then follow the steps on the ROI tutorial (ie, aparcstats2table and mri_glmfit with --table input).
On 11/3/17 4:08 PM, Bruce Fischl wrote:
Hi Mohamed
Doug is away this week and can give you a more details answer next week. Certainly you could use mris_anatomical_stats -l <BA label file name> to compute the volume/thickness/area for each subject then do whatever GLM analysis you want outside of FS.
cheers Bruce
On Fri, 3 Nov 2017, m.bahri@uliege.be wrote:
Dear All, Does anyone have an answer to the following VBM question?
Many thanks in advance, Regards
-----Mail original----- De: "Mohamed Ali Bahri" m.bahri@uliege.be À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM Objet: [Freesurfer] VBM question
Dear Freesurfer users,
I would like to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. I tried to do that with Qdec tool but unfortunately Qdec does not load the Brodmann areas stat list. I am wondering if I could use the GLM formalism with of course regressing out the ITV. Any suggestion/advice will be very welcome.
Many thanks in advance,
Best regards,
Mohamed
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.
-- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri@uliege.be
No, sorry. You can always use the command line stream (mris_preproc, mri_surf2surf, create your fsgd file with your covariates of interest, and then run mri_glmfit)
On 11/10/17 4:13 AM, m.bahri@uliege.be wrote:
Dear Douglas,
Thank you very much for you answer. I checked all the aparc stat files (/Freesurfer/subjects/subjectID/stats/lh.aparc.stats; lh.aparc.a2009s.stats ....) and my region of interest "perirhinal" (region extending on BA35 and BA36 areas) is only present on the lh/rh.BA.stats files (/Freesurfer/subjects/subjectID/stats/lh.BA.stats and rh.BA.stats). I use Freesurfer version 5.3. When using Qdec tool the only uploadable files are .aparc files. Is it possible to upload also the regions of BA.stats files?
Best regards, Mohamed
----- Mail original ----- De: "Douglas N Greve" greve@nmr.mgh.harvard.edu À: "Mohamed Ali Bahri" m.bahri@uliege.be, freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 6 Novembre 2017 23:44:43 Objet: Re: [Freesurfer] Trans. : VBM question
Hi Mohamed, please remember to post to the list. As for your question, what aparc files are you looking at? Those measures are in, eg, lh.aparc.stats
On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote:
Dear Douglas,
Many thanks for your answer!
We are interested on one region belonging to the Brodmann areas "Perirhinal". Cortical thickness as well as volume values appear on the BA stat list and not on the aparc or aseg lists. Does the ROI-based analysis could be used for this BA region?
Best regards,
Mohamed
On 05/11/2017 18:46, Douglas Greve wrote:
Do you just want to do an ROI analysis? Or do you want to do a voxel-based analysis? If ROI-based, then follow the steps on the ROI tutorial (ie, aparcstats2table and mri_glmfit with --table input).
On 11/3/17 4:08 PM, Bruce Fischl wrote:
Hi Mohamed
Doug is away this week and can give you a more details answer next week. Certainly you could use mris_anatomical_stats -l <BA label file name> to compute the volume/thickness/area for each subject then do whatever GLM analysis you want outside of FS.
cheers Bruce
On Fri, 3 Nov 2017, m.bahri@uliege.be wrote:
Dear All, Does anyone have an answer to the following VBM question?
Many thanks in advance, Regards
-----Mail original----- De: "Mohamed Ali Bahri" m.bahri@uliege.be À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM Objet: [Freesurfer] VBM question
Dear Freesurfer users,
I would like to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. I tried to do that with Qdec tool but unfortunately Qdec does not load the Brodmann areas stat list. I am wondering if I could use the GLM formalism with of course regressing out the ITV. Any suggestion/advice will be very welcome.
Many thanks in advance,
Best regards,
Mohamed
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.
-- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri@uliege.be
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
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m.bahri＠uliege.be