Re: [Freesurfer] ERROR selxavg-sess
Hi Keta, this is a pretty old version. Are you sure you don't want to upgrade? The ipr is the "in-plane resolution" stored in the seq.info file in the bold directory. Newer versions don't use this anymore. doug On Thu, 8 Jul 2010, ±¬Ìî¸ÂÀ wrote: Hi,Freesurfers I'm going to analyze the functional data. By now I finished reconstruction of anatomical data and maiking hierarchy, mc-sess,spatialsmooth-sess,inorm-sess,mkanalysis-sess and fslregister. But selxavg-sess output following ERROR. please tell me about -ipr. Keta ke...@localhost[retino1] % mkanalysis-sess.new -analysis retino -TR 2 -paradigm para.para -designtype blocked -funcstem fmcs -nconditions 4 -timewindow 34 -motioncor -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force Completed successfully ke...@localhost[retino1] % selxavg-sess -analysis retino -s sekiguchi001 -df sessdirfile -noomnibus INFO: WhitenFlag = 0 -- selxavg-sess logfile is /home/kenta/data/sessions/retino1/log/selxavg-sess-bold-retino-100708112251.log -- --- /home/kenta/data/sessions/retino1/sekiguchi001 2010ǯ 7·î 8Æü ÌÚÍËÆü 11:22:51 JST INFO (sekiguchi001): RunList = 001 002 003 004 /home/kenta/data/sessions/retino1/sekiguchi001/bold selxavg2 -TR 2 -parname para.para -o retino/h -i 001/fmcs -i 002/fmcs -i 003/fmcs -i 004/fmcs -cfg /home/kenta/data/sessions/retino1/retino/analysis.cfg -ipr here --- Parsing Config File: /home/kenta/data/sessions/retino1/retino/analysis.cfg -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: flag -ipr requires one argument ERROR (/home/kenta/data/sessions/retino1/sekiguchi001): selxavg failed -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ERROR selxavg-sess
Hi,Freesurfers I'm going to analyze the functional data. By now I finished reconstruction of anatomical data and maiking hierarchy, mc-sess,spatialsmooth-sess,inorm-sess,mkanalysis-sess and fslregister. But selxavg-sess output following ERROR. please tell me about -ipr. Keta ke...@localhost[retino1] % mkanalysis-sess.new -analysis retino -TR 2 -paradigm para.para -designtype blocked -funcstem fmcs -nconditions 4 -timewindow 34 -motioncor -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force Completed successfully ke...@localhost[retino1] % selxavg-sess -analysis retino -s sekiguchi001 -df sessdirfile -noomnibus INFO: WhitenFlag = 0 -- selxavg-sess logfile is /home/kenta/data/sessions/retino1/log/selxavg-sess-bold-retino-100708112251.log -- --- /home/kenta/data/sessions/retino1/sekiguchi001 2010年 7月 8日 木曜日 11:22:51 JST INFO (sekiguchi001): RunList = 001 002 003 004 /home/kenta/data/sessions/retino1/sekiguchi001/bold selxavg2 -TR 2 -parname para.para -o retino/h -i 001/fmcs -i 002/fmcs -i 003/fmcs -i 004/fmcs -cfg /home/kenta/data/sessions/retino1/retino/analysis.cfg -ipr here --- Parsing Config File: /home/kenta/data/sessions/retino1/retino/analysis.cfg -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: flag -ipr requires one argument ERROR (/home/kenta/data/sessions/retino1/sekiguchi001): selxavg failed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer file
Hello, Freesurfer experts I'v got a work with the freesurfer files. As we all know, there are many files in the freesurfer subject directory, and each file has its usage. My question is, what's the particular usage for each of these files and how can I read these files using Matlab or any other softwares rather than the freesurfer tools? Is there a list for this? Thanks in advance. -- Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA ___ 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] probabilistic white matter mask
Hi Folks, I believe that I can create a binary white matter mask using "mri_wmfilter". I was wondering if there is a way to create a probabilistic white matter mask ? (for each voxel, I would like to obtain the probability of it being white matter) I did a search on the mailing list and found the following related message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11786.html The message suggests to use "-write_probs" flag with the mri_ca_label command but I dont see this flag as on option in the usage instructions for mri_ca_label. If this is the right way, should i just add "-write_probs wm.mgz" to mri_ca_label to get a probablistic white matter mask ? Thanks Mehul ___ 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] editing labels in tksurfer
Hi Everyone, I remember a post in March when Allison referred someone to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit and I think this will be really helpful for me if I can figure out how to make it work. I have a scan with corpus callosum bleeding into the caudalanteriorcingulate. When I try to change the label, I am able to select the region by clicking on it. However, when I try to "Draw a complete outline path that encloses the desired "incursion"", every time I click to draw the path, the image refreshes. Here are the instructions: "Create outline path: * Possibly start with Edit > Unmark all vertices * Make a series of clicks along the desired outline path. tksurfer shows marked vertices." Is "create outline path" the same as "Make Path" on the TkSurfer tools box? What would make the decision between "Possibly start with Edit > Unmark all vertices" and not doing that? I succeeded once in getting the path drawn, but have no luck replicating that. Also, when I tried to relabel the part inside the path, I was able to turn it into label = "None" or turn 90% of the brain into caudalanteriorcingulate. I'm missing something really simple here - help, please. Also - can this be done also on the pial surface using this command? I can see the boundaries better on this view than on the inflated tksurfer $i lh pial -annotation aparc Thanks for any help - let me know if you need more information Helen Keefe ___ 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] entorhinal surface and wm intensity
Hi Derin, that is odd, not sure what's going on either with your wrinkles or the loss of surface after editing. Can you upload the pre and post edited datasets for us to look at? Bruce On Thu, 1 Jul 2010, Derin Cobia wrote: > I have questions regarding two issues we've run into processing dementia and > age-matched healthy subjects: > > 1. For several of our subjects, we've noticed that an isolated region of the > entorhinal pial surface becomes 'indented' towards the white surface (see in > RH in attached pics- P5b*). Not sure what's going, I've tried to correct it > by removing any extraneous neighboring voxels or other 'anomalies' (no voxel > gaps in the wm volumes from lesions, etc). It almost reminds me of the > insula 'spike' a few versions back. Thoughts? > > 2. After re-running a subject for cp and wm edits, the resulting white (and > consequently pial) surface has become inaccurate for large portions of the > anterior temporal and frontal lobes, but just in the LH (attached pics- > P8b*). To clarify, this was not the case after the data's initial run, only > once edits were made and incorporated. We've run into this before, but only > after editing a subject multiple times (3-4x, thus more recons), or > 'updating' subjects to a new FS version (e.g., re-running v4.1.0 data with > v4.5.0). Are edits changing the intensity threshold? It's odd that it's > asymmetric. > > Any help/thoughts would be appreciated, thanks. > > -Derin > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Help on QDEC: Obtainign mean, sd and p-values from glm result
If you just want a mean and sd over a region you can run mri_segstats with the --annot option. What do you mean by a p-value for a region? doug Fernanda Palhano wrote: > > Hello, > > > I've just started using freesurfer. I've reading the mail list wich > helps me a lot, but > I can't find how I can obtain a table with the values of my glm analysis. > For exemple, in the Qdec's tutorial I have a surface that answer the > question "Does > the correlation between thickness and age differ from zero?" It's > possible to see this data like > a table: > region mean sdp-value > precentral xx x > > Or at least obtain those values individually? > > thank you very much in advance, > Fernanda > > > > ___ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] manual corregistration...
co-registration of what with what? tkregister2 is for function/diffusion to structure On Wed, 7 Jul 2010, Gonzalo Rojas wrote: > Hi: > > How can I do a manual corresistration with freesurfer ?... > > Sincerely, > > > ___ 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] manual corregistration...
Hi: How can I do a manual corresistration with freesurfer ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Help on QDEC: Obtainign mean, sd and p-values from glm result
Hello, I've just started using freesurfer. I've reading the mail list wich helps me a lot, but I can't find how I can obtain a table with the values of my glm analysis. For exemple, in the Qdec's tutorial I have a surface that answer the question "Does the correlation between thickness and age differ from zero?" It's possible to see this data like a table: region mean sdp-value precentral xx x Or at least obtain those values individually? thank you very much in advance, Fernanda ___ 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] subcortical segmentation
I have used: recon-all -s -subcortseg which runs through step 11 (-calabel), with the understanding re: accuracy that Bruce pointed out. -Julie On 7/7/10 8:07 AM, "Bruce Fischl" wrote: > Hi Salem, > > yes, you can run any individual options in recon-all. See the -help output > and run it through step 11 if you want. Note that we do use the surfaces to > improve the aseg accuracy at the very end, so you'll be giving that up. > > cheers > Bruce > On > Wed, 7 Jul 2010, Hannoun wrote: > >> >> >> Hi, >> >> I am a new user of freesurfer. Is it possible to do just the volumetric >> processing stages without the surface processing stages? >> >> In fact what I want is to segment the subcortical structures. >> >> Is there a command line for this purpose only or should we run all the >> recon-all steps? >> >> Thank you for your help >> >> Salem >> >> >> >> >> >> > ___ > 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] Qdec - problem with the Generate Stats Data Import button.
Hi Krish,
Thank you for your reply.
Unfortunately none of these did work (but now I've an up-to-date environment
at least).
But the IT/research engineer in the lab found that it was "just" my
environment PYTHONHOME and PYTHONPATH which were pointing at a bad
directory.
After unsetting these two env, it works perfectly fine.
Thanks for your help,
Gaëlle.
-Message d'origine-
De : Krish Subramaniam [mailto:kr...@nmr.mgh.harvard.edu]
Envoyé : mardi 6 juillet 2010 17:47
À : Gaëlle Leroux
Cc : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Qdec - problem with the Generate Stats Data Import
button.
Hi Gaelle
This seems to be an error due to Python's "warning" module being
deprecated in Python 2.6. I'll update the sources so as to accommodate
this change.
Meanwhile, the quickest fix is to open up
nano $FREESURFER_HOME/bin/asegstats2table
and comment out the following lines ( put a "#" at the start of the
line ).. i.e change
import warnings
warnings.filterwarnings('ignore', '.*negative int.*')
to
#import warnings
#warnings.filterwarnings('ignore', '.*negative int.*')
and see whether it works.
Best
Krish
On Jul 6, 2010, at 4:31 AM, Gaëlle Leroux wrote:
> Dear FS,
>
> I'm basically stocked with a problem when I press the "Generate
> Stats Data Import" in the Qdec GUI.
> I got the following error message as in the attached file.
> I'm running FS using a python 2.6 version.
> It seems that I do have a problem with the asegstat2table command
> line but I don't understand why...
> Any advice, please?
>
> Many thanks in advance for your help.
>
> Sincerely,
> Gaëlle Leroux.
>
> ___
> 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] RV: FREESURFER
Hi Santiago, if the talairach is correct (you can verify this in tkmedit or tkregister2) then you can just turn the auto checking of the tal transform off in recon-all. cheers Bruce On Wed, 7 Jul 2010, SANTIAGO GONZALEZ CALERO wrote: > >> Good morning,I am working on brain segmentation using freesurfer > program. >> I wonder if it is possible to turn an initial image with some tool > freesurfer. Because my problem is that when I start to perform > segmentation in freesurfer, I get an error and I think that is because > dicom image format is a little crooked. If you can not rotate with > tkmedit or similar tool. >> The error I get is as follows: >> >> ERROR >>cp transforms/talairach.auto.xfm > transforms/talairach.xfm >> >># >>#...@# >>Talairach Failure Detection Tue Jun 22 04:45:20 EDT > 2010 >>/usr/local/freesurfer/subjects/ome/mri >> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> >> >>ERROR: talairach_afd: Talairach Transform: > transforms/talairach.xfm ***FAILED*** >>(p=0.0063, pval=0. < threshold=0.0050) >> >> I have tested the segmentation with another patient and gives me the > following error. >> >> ERROR >> >> FINAL ITERATIVE TEMPLATE DEFORMATION >>Compute Local values csf/gray >> Fine Segmentation...44 iterations >> mghRead: encountered error executing: 'zcat > /usr/local/freesurfer/subjects/francia/mri/T1.mgz',frame -1, errno 12 >> >>mri_strip_skull: done peeling brain >> >> Brain Size = 1260141 voxels, voxel volume = 1.000 mm3 >> = 1260141 mmm3 = 1260.141 cm3 >> >> mri_watershed Error: read failed >> >> Linux freesurfer-virtual 2.6.28-19-generic #61-Ubuntu > SMP Wed May 26 23:35:15 UTC 2010 i686 GNU/Linux >> >> recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT > 2010 >> >> Do not know if these errors can be solved with some kind of tool or if > on the contrary are due to initial images of patients are slightly > slanted, and if the same could reorient vertically. >> Thank you very much. A greeting. >> Attentively > > > ___ > 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] subcortical segmentation
Hi Salem, yes, you can run any individual options in recon-all. See the -help output and run it through step 11 if you want. Note that we do use the surfaces to improve the aseg accuracy at the very end, so you'll be giving that up. cheers Bruce On Wed, 7 Jul 2010, Hannoun wrote: > > > Hi, > > I am a new user of freesurfer. Is it possible to do just the volumetric > processing stages without the surface processing stages? > > In fact what I want is to segment the subcortical structures. > > Is there a command line for this purpose only or should we run all the > recon-all steps? > > Thank you for your help > > Salem > > > > > > ___ 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] RV: FREESURFER
> Good morning,I am working on brain segmentation using freesurfer program. > I wonder if it is possible to turn an initial image with some tool freesurfer. Because my problem is that when I start to perform segmentation in freesurfer, I get an error and I think that is because dicom image format is a little crooked. If you can not rotate with tkmedit or similar tool. > The error I get is as follows: > > ERROR >cp transforms/talairach.auto.xfm transforms/talairach.xfm > ># >#...@# >Talairach Failure Detection Tue Jun 22 04:45:20 EDT 2010 >/usr/local/freesurfer/subjects/ome/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > >ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** >(p=0.0063, pval=0. < threshold=0.0050) > > I have tested the segmentation with another patient and gives me the following error. > > ERROR > > FINAL ITERATIVE TEMPLATE DEFORMATION >Compute Local values csf/gray > Fine Segmentation...44 iterations > mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/francia/mri/T1.mgz',frame -1, errno 12 > >mri_strip_skull: done peeling brain > > Brain Size = 1260141 voxels, voxel volume = 1.000 mm3 > = 1260141 mmm3 = 1260.141 cm3 > > mri_watershed Error: read failed > > Linux freesurfer-virtual 2.6.28-19-generic #61-Ubuntu SMP Wed May 26 23:35:15 UTC 2010 i686 GNU/Linux > > recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT 2010 > > Do not know if these errors can be solved with some kind of tool or if on the contrary are due to initial images of patients are slightly slanted, and if the same could reorient vertically. > Thank you very much. A greeting. > Attentively ___ 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] subcortical segmentation
Hi, I am a new user of freesurfer. Is it possible to do just the volumetric processing stages without the surface processing stages? In fact what I want is to segment the subcortical structures. Is there a command line for this purpose only or should we run all the recon-all steps? Thank you for your help Salem <>___ 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.
