Re: [Freesurfer] PVE correction tool within the V 6 beta
Dear Greve, Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some unclear options (e.g. --mgx .01) Could you please explain which method is used for the pve correction and how can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of all regions? Many thanks for your help, Best, Mohamed - Mail original - De: "Douglas Greve" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 28 Septembre 2015 17:49:49 Objet: Re: [Freesurfer] PVE correction tool within the V 6 beta I'm still putting all the documentation together, but you can start with the instructions below. They are assuming you will use kinetic modeling. If you have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 not needed. Let me know and I can give you further instructions. doug 1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1. 3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i tac.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. --km-hb specifies the highbinding region for MRTM2. --km-ref specifies the reference region. --mgx specifies to output a muller-gartner map (not necessary for GTM ROI analysis). 4. For the GTM (ROI) MRTM1 KM analysis, you would then run mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz where time.dat is a text file withe acquisition time of each time point in the tac. 5. For the MRTM2 analysis set k2p = `cat mrtm1/k2prime.dat` mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o mrtm1 --no-est-fwhm --nii.gz If you want to run a voxel-wise analysis, then you can use the mgx volume as input (--y). Probably you'll want to sample this to the surface using mri_vol2surf and the registration file aux/anat2pet.lta, then smooth on the surface On 9/28/15 11:38 AM, Mohamed Ali Bahri wrote: > Dear Expert, > > Are there any explanation (steps to follow) about the use of FreeSurfer > (version 6 beta) to correct for the partial volume effect (PET dynamic > data)? > > Many thanks in advance, > > Best, > > Mohamed > ___ 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] FreeSurfer pve correction tool
Dear FreeSurfer Experts, Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6? Many thanks in advance, Best, Mohamed ___ 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] Recon-all error
Dear Experts, I have the following error with recon-all (freesurfer v 5.3) in the orig_nu.log file. Could anyone help to solve the problem? Many thanks, Mohamed Iteration 1 Fri Feb 26 14:13:20 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.20504/nu0.mnc ./tmp.mri_nu_correct.mni.20504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20504/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /usr/local/freesurfer/mni/share/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct ___ 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] Trans. : VBM question
Dear All, Does anyone have an answer to the following VBM question? Many thanks in advance, Regards -Mail original- De: "Mohamed Ali Bahri" À: "Freesurfer support list" 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 -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.ba...@uliege.be ___ 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
Re: [Freesurfer] Trans. : VBM question
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" À: "Mohamed Ali Bahri" , 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 >> 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.ba...@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" À: "Freesurfer support list" 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.ba...@uliege.be -- 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] freesurfer segmentation: perirhinal Roi
Dear Bruce, Many thanks for you answer! I am trying to rerun the cortical reconstruction with the version 6.0 but I got the following error. May I have a license for this Freesurfer version 6.0? Thanks a lot for your kind help! Best regards, Mohamed -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi Hi Mohamed I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed. cheers Bruce On Tue, 9 Jan 2018, m.ba...@uliege.be wrote: > Dear Freesurfer experts, > > We would like to use volume and cortical thickness measures obtained for the > perirhinal cortex in Freesurfer 5. When checking the region that has been > segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not > seem to cover the entire cortical thickness of the region. On the coronal > slice shown in example (attached file), one can see that there are still a > few voxels of gray matter between the external border of the ROI and the > external boundary of the cortex. How reliable is this segmentation? Is there > a reason why the ROI appears so thin? > > Many thanks in advance, > > Best regards, > > > ___ 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, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.ba...@uliege.be Tel : + 32-4-3662304 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Dear Bruce, Many thanks for your kind help! I put the subject data on your ftp site (s8201.tar). Best regards, Mohamed - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi Hi Mohamed if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.ba...@uliege.be wrote: > Dear Bruce, > > Attached is the screen shot of the results of the segmentation of the > perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented > Roi does not cover the entire cortical thickness of the region. Is there any > other alternative to get a better segmentation of this region? > > Many thanks in advance, > > Best regards, > > Mohamed > > - Mail original - > De: "Bruce Fischl" > À: "Freesurfer support list" > Envoyé: Mardi 9 Janvier 2018 14:50:16 > Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi > > Hi Mohamed > > I'm pretty sure this was an issue with the ribbon-filling in V5 that is > better in V6. Try using it and see if it is fixed. > > cheers > Bruce > On Tue, 9 Jan 2018, > m.ba...@uliege.be wrote: > >> Dear Freesurfer experts, >> >> We would like to use volume and cortical thickness measures obtained for the >> perirhinal cortex in Freesurfer 5. When checking the region that has been >> segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not >> seem to cover the entire cortical thickness of the region. On the coronal >> slice shown in example (attached file), one can see that there are still a >> few voxels of gray matter between the external border of the ROI and the >> external boundary of the cortex. How reliable is this segmentation? Is there >> a reason why the ROI appears so thin? >> >> Many thanks in advance, >> >> Best regards, >> >> >> > ___ > 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. -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.ba...@uliege.be Tel : + 32-4-3662304 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Dear Bruce, Thank you for your answer! I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder). If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC? Thank you very much in advance, Best regards, Mohamed - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Vendredi 19 Janvier 2018 16:53:18 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi Hi Mohamed how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me? cheers Bruce On Fri, 19 Jan 2018, m.ba...@uliege.be wrote: > Dear Bruce, > > Many thanks for your kind help! > > I put the subject data on your ftp site (s8201.tar). > > Best regards, > > Mohamed > > > > - Mail original - > De: "Bruce Fischl" > À: "Freesurfer support list" > Envoyé: Jeudi 18 Janvier 2018 16:37:10 > Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi > > Hi Mohamed > > if you tar, gzip and ftp this subject to our ftp site we will take a look > cheers > Bruce > On > Thu, 18 Jan 2018, m.ba...@uliege.be wrote: > >> Dear Bruce, >> >> Attached is the screen shot of the results of the segmentation of the >> perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented >> Roi does not cover the entire cortical thickness of the region. Is there any >> other alternative to get a better segmentation of this region? >> >> Many thanks in advance, >> >> Best regards, >> >> Mohamed >> >> - Mail original - >> De: "Bruce Fischl" >> À: "Freesurfer support list" >> Envoyé: Mardi 9 Janvier 2018 14:50:16 >> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >> >> Hi Mohamed >> >> I'm pretty sure this was an issue with the ribbon-filling in V5 that is >> better in V6. Try using it and see if it is fixed. >> >> cheers >> Bruce >> On Tue, 9 Jan 2018, >> m.ba...@uliege.be wrote: >> >>> Dear Freesurfer experts, >>> >>> We would like to use volume and cortical thickness measures obtained for >>> the perirhinal cortex in Freesurfer 5. When checking the region that has >>> been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does >>> not seem to cover the entire cortical thickness of the region. On the >>> coronal slice shown in example (attached file), one can see that there are >>> still a few voxels of gray matter between the external border of the ROI >>> and the external boundary of the cortex. How reliable is this segmentation? >>> Is there a reason why the ROI appears so thin? >>> >>> Many thanks in advance, >>> >>> Best regards, >>> >>> >>> >> ___ >> 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. > ___ 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, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.ba...@uliege.be Tel : + 32-4-3662304 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman
Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Dear Bruce, Thank you very much for your kind help! Best regards - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive). cheers Bruce On Mon, 22 Jan 2018, m.ba...@uliege.be wrote: > Dear Bruce, > > Thank you for your answer! > > I just display the "T1.mgz" image (mri folder) using Freeview and then loaded > the "lh/rh.perirhinal_exvivo.label" rois (label folder). > > If this is not the good way to do it, please, could you explain more the > procedure? What do you mean by MT and PC? > > Thank you very much in advance, > > Best regards, > > Mohamed > > > - Mail original - > De: "Bruce Fischl" > À: "Freesurfer support list" > Envoyé: Vendredi 19 Janvier 2018 16:53:18 > Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi > > Hi Mohamed > > how are you visualizing the MT or PC ROIs. Did you sample them into the > volume? If so, can you tell me where the file ROIs are in the data you > sent me? > > cheers > Bruce > On Fri, 19 Jan 2018, m.ba...@uliege.be wrote: > >> Dear Bruce, >> >> Many thanks for your kind help! >> >> I put the subject data on your ftp site (s8201.tar). >> >> Best regards, >> >> Mohamed >> >> >> >> - Mail original - >> De: "Bruce Fischl" >> À: "Freesurfer support list" >> Envoyé: Jeudi 18 Janvier 2018 16:37:10 >> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >> >> Hi Mohamed >> >> if you tar, gzip and ftp this subject to our ftp site we will take a look >> cheers >> Bruce >> On >> Thu, 18 Jan 2018, m.ba...@uliege.be wrote: >> >>> Dear Bruce, >>> >>> Attached is the screen shot of the results of the segmentation of the >>> perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented >>> Roi does not cover the entire cortical thickness of the region. Is there >>> any other alternative to get a better segmentation of this region? >>> >>> Many thanks in advance, >>> >>> Best regards, >>> >>> Mohamed >>> >>> - Mail original - >>> De: "Bruce Fischl" >>> À: "Freesurfer support list" >>> Envoyé: Mardi 9 Janvier 2018 14:50:16 >>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >>> >>> Hi Mohamed >>> >>> I'm pretty sure this was an issue with the ribbon-filling in V5 that is >>> better in V6. Try using it and see if it is fixed. >>> >>> cheers >>> Bruce >>> On Tue, 9 Jan 2018, >>> m.ba...@uliege.be wrote: >>> Dear Freesurfer experts, We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin? Many thanks in advance, Best regards, >>> ___ >>> 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. >> > ___ > 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 > addres
Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Dear Bruce, Many thanks for you kind answer. I sampled the perirhinal roi label into the volume using the suggested command line: "mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o lh.perirhinal.volume.nii --hemi lh --identity". The obtained mask seems to cover well the perirhinal structure. Now, I calculate the perirhinal volmue (mm3) based on the obtained mask but I found that the obtained value does not match the one obtained during the Freesurfer cortical reconstruction (values in the stat folder: files : rh/lh-BA_exvivo.stats). did I messed something? Thank you very much in advance, Best regards, Mohamed - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive). cheers Bruce On Mon, 22 Jan 2018, m.ba...@uliege.be wrote: > Dear Bruce, > > Thank you for your answer! > > I just display the "T1.mgz" image (mri folder) using Freeview and then loaded > the "lh/rh.perirhinal_exvivo.label" rois (label folder). > > If this is not the good way to do it, please, could you explain more the > procedure? What do you mean by MT and PC? > > Thank you very much in advance, > > Best regards, > > Mohamed > > > - Mail original - > De: "Bruce Fischl" > À: "Freesurfer support list" > Envoyé: Vendredi 19 Janvier 2018 16:53:18 > Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi > > Hi Mohamed > > how are you visualizing the MT or PC ROIs. Did you sample them into the > volume? If so, can you tell me where the file ROIs are in the data you > sent me? > > cheers > Bruce > On Fri, 19 Jan 2018, m.ba...@uliege.be wrote: > >> Dear Bruce, >> >> Many thanks for your kind help! >> >> I put the subject data on your ftp site (s8201.tar). >> >> Best regards, >> >> Mohamed >> >> >> >> - Mail original - >> De: "Bruce Fischl" >> À: "Freesurfer support list" >> Envoyé: Jeudi 18 Janvier 2018 16:37:10 >> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >> >> Hi Mohamed >> >> if you tar, gzip and ftp this subject to our ftp site we will take a look >> cheers >> Bruce >> On >> Thu, 18 Jan 2018, m.ba...@uliege.be wrote: >> >>> Dear Bruce, >>> >>> Attached is the screen shot of the results of the segmentation of the >>> perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented >>> Roi does not cover the entire cortical thickness of the region. Is there >>> any other alternative to get a better segmentation of this region? >>> >>> Many thanks in advance, >>> >>> Best regards, >>> >>> Mohamed >>> >>> - Mail original - >>> De: "Bruce Fischl" >>> À: "Freesurfer support list" >>> Envoyé: Mardi 9 Janvier 2018 14:50:16 >>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >>> >>> Hi Mohamed >>> >>> I'm pretty sure this was an issue with the ribbon-filling in V5 that is >>> better in V6. Try using it and see if it is fixed. >>> >>> cheers >>> Bruce >>> On Tue, 9 Jan 2018, >>> m.ba...@uliege.be wrote: >>> Dear Freesurfer experts, We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin? Many thanks in advance, Best regards, >>> ___ >>> 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 se
