Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Visualization of FreeSurfer-defined ROI
by Simmons, Andy 08 Nov '11

08 Nov '11

Dear Doug, What would the equivalent process for a surface rather than a volume ? Best wishes, Andy SImmons Date: Fri, 04 Nov 2011 17:30:47 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Visulaization of FreeSurfer-defined ROI To: Jade <jadeinny8(a)gmail.com<mailto:jadeinny8@gmail.com>> Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <4EB45987.2040001(a)nmr.mgh.harvard.edu<mailto:4EB45987.2040001@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Try running mri_binarize with the --match option. The match value should be the id number for your ROI as defined in $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, left hippo is 17). You can then load this as a segmentation or as an overlay in tkmedit. doug Jade wrote: > Hello Freesurfer experts, > > I am a beginner in using Freesurfer. > > I want to make a figure illustrates a specific area of ROIs (e.g., > lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? > > Thanks in advance! ---- Dr Andy Simmons Reader in Neuroimaging & Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simmons(a)kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-… ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 [cid:image001.png@01CC9E47.37F065F0]<http://msc-neuroimaging.com/>

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Upgraded Freesurfer: old version no longer working + recon-all error in 5.1
by Jennifer Addicks 08 Nov '11

08 Nov '11

Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh --------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. 2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs: Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 Any ideas on what might be causing this error? I have 4 GB memory. thanks, Jennifer Addicks University of Ottawa

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Fwd: A question about recon-all
by nooshin n.zade 08 Nov '11

08 Nov '11

Dear Freesurfer Group I have found a problem in running my subjects. With "recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N?" I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance. INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: ---------------------------------------------------------- ------------------------------ SUBJECT N3237c HEMI lh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ ---------------------------------------------------------- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * * -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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norm.mgz
by YUMI MAEDA 08 Nov '11

08 Nov '11

Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI

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Recon-all step estimate
by Pedro Paulo de Magalhães Oliveira Junior 08 Nov '11

08 Nov '11

Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr

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surface cnr
by Michael Harms 08 Nov '11

08 Nov '11

Hello, What is the difference between the mris_ms_surface_CNR and mri_cnr functions? (I couldn't find any descriptive info for either). And are either of them useful for identifying datasets with "poor" gray/white/csf contrast? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Freesurfer on CentOS 6.
by SHRIKANTH KULASHEKHAR 08 Nov '11

08 Nov '11

Hi, The recommed platform for Freesurfer is CentOS 4. Can anyone advice on how stable the Freesurfer v5.1.0 will be on CentOS 6 ? We need this information to setup a new server. Thanks in advance. Shrikanth

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Affine Matrix Conversions
by Matt Glasser 07 Nov '11

07 Nov '11

Hi, I am wondering what tools FreeSurfer has to convert between different affine matrix formats. For example, if I had a talairach.xfm that did a better job than talairach.lta, is there a way to convert from one to the other? What about FSL FLIRT matricies? Can these be interconverted with .lta? Thanks, Matt.

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Re: [Freesurfer] different interpolation smoothing in conform step
by Irene Altarelli 07 Nov '11

07 Nov '11

Dear Martin and all, I had actually checked the RAS coordinates for all of my subjects and timepoints, and the one I mentioned is the only one in which the rotation is present. I created a uchar image from rawavg.mgz and tried to run recon-all from that without the motioncor step and without talairach (creating talairach.xfm manually from scratch using tkregister2), but recon-all crashes during mri_nu_correct (see error below). One strange observation: I had been running this subject in version 5.0 previously and noticed that, although the RAS coordinates and transform are the same as the ones I get in version 5.1, I do not see any smoothing effect when comparing rawavg.mgz and orig.mgz. I guess the best we can do at this stage is to manually edit the input nii file so that no rotation is coded in there (by changing the sform/qform as suggested by Michael Harm) - unless you have other suggestions... Thanks very much again for your help, Irene $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.22469/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (-0.0436194, 0, 0.999048) k_ras = (0.999048, 0, 0.0436194) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz MRIvoxelToTalairachVoxel: unsupported slice direction 1 MRIvoxelToTalairachVoxel: unsupported slice direction 1 Numerical result out of range MRIvoxelToTalairachVoxel: unsupported slice direction 1 Numerical result out of range MRIvoxelToTalairachVoxel: unsupported slice direction 1 Numerical result out of range Le vendredi 04 novembre 2011 à 16:17 -0400, Martin Reuter a écrit : > Irene, > > I don't really know why the RAS coordinates are slightly rotated. I > checked and they are orthogonal. I don't know where this comes from > (autoalign on the scanner, but then why would it be only in one of your > volumes). > > Maybe Doug knows a trick how to avoid the interpolation as it seems > unnecessary? > > > Also, when you say you checked the other subject, did you look at the > images, or did you check the RAS coordinates in the mri_info output. It > can be that rotation is small and you won't see it the image but it is > still there. The RAS xform x_r,x_a,x_s, y_r, y_a, y_s and z_r z_a z_s > should only be +-1 or zero. > > Best, Martin > > > On Fri, 2011-11-04 at 17:46 +0100, Irene.Altarelli(a)ens.fr wrote: > > Dear Martin, > > > > I have a single scan per session, so no averaging. Also, this is the only image > > in my longitudinal data for which I am encountering this problem. I have > > checked all other subjects and none of them is rotated/smoothed. > > > > I am not sure I understand precisely why this scan needs to be rotated, is it to > > establish RAS coordinates' center and axes? Do you think there is a way I can > > fix it? I don't have many subjects in this protocol, so dropping one would be a > > real pity. > > > > Thanks very much again for your help. > > Best, > > Irene > > > > > > > > > > > > Selon Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: > > > > > Hi Irene, > > > > > > the voxel sizes are isotropic 1mm (which is good). However for some > > > reason the first image is slightly rotated while the second is perfectly > > > aligned with the axes. Therefore the first gets interpolated while the > > > second stays the same. That explains the different smoothing. > > > > > > Now the question is why is one image different. Do you collect a single > > > scan for each session or are you averaging several within-session scans? > > > You should look at other subjects and try to find out if and why > > > specific time points are slightly rotated. > > > > > > By the way this is a good example how to potentially mess up a > > > longitudinal study. If for example one of the time points is always (or > > > more frequently) rotated because of a different protocol the study would > > > be severely biased. So it is good that you are checking this. > > > > > > Best, Martin > > > > > > > > > On Fri, 2011-11-04 at 10:28 +0100, Irene.Altarelli(a)ens.fr wrote: > > > > Dear Martin, > > > > > > > > the RAS coordinates and voxel to ras transforms are indeed slightly > > > different. > > > > Should I change this and if so, how? > > > > > > > > Please find the output of mri_info for each of the two acquisitions at the > > > end > > > > of this email. > > > > > > > > Thanks again! > > > > Irene > > > > > > > > > > > > > > > > > *********************************************************************************** > > > > > > > > Volume information for gsTP1/mri/rawavg.mgz > > > > type: MGH > > > > dimensions: 256 x 256 x 176 > > > > voxel sizes: 1.0000, 1.0000, 1.0000 > > > > type: FLOAT (3) > > > > fov: 256.000 > > > > dof: 0 > > > > xstart: -128.0, xend: 128.0 > > > > ystart: -128.0, yend: 128.0 > > > > zstart: -88.0, zend: 88.0 > > > > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > > > > degrees > > > > nframes: 1 > > > > PhEncDir: UNKNOWN > > > > ras xform present > > > > xform info: x_r = 0.0000, y_r = -0.0436, z_r = 0.9990, c_r = > > > -3.5493 > > > > : x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = > > > 12.8739 > > > > : x_s = 0.0000, y_s = 0.9990, z_s = 0.0436, c_s = > > > -16.0490 > > > > > > > > talairach xfm : > > > > Orientation : PSR > > > > Primary Slice Direction: sagittal > > > > > > > > voxel to ras transform: > > > > 0.0000 -0.0436 0.9990 -85.8823 > > > > -1.0000 0.0000 0.0000 140.8739 > > > > 0.0000 0.9990 0.0436 -147.7657 > > > > 0.0000 0.0000 0.0000 1.0000 > > > > > > > > voxel-to-ras determinant -1 > > > > > > > > ras to voxel transform: > > > > -0.0000 -1.0000 -0.0000 140.8739 > > > > -0.0436 0.0000 0.9990 143.8789 > > > > 0.9990 -0.0000 0.0436 92.2460 > > > > 0.0000 0.0000 0.0000 1.0000 > > > > > > > > > > > > > > > > > > > > > > > > > *********************************************************************************** > > > > > > > > > > > > > > > > Volume information for gsTP2/mri/rawavg.mgz > > > > type: MGH > > > > dimensions: 256 x 256 x 176 > > > > voxel sizes: 1.0000, 1.0000, 1.0000 > > > > type: FLOAT (3) > > > > fov: 256.000 > > > > dof: 0 > > > > xstart: -128.0, xend: 128.0 > > > > ystart: -128.0, yend: 128.0 > > > > zstart: -88.0, zend: 88.0 > > > > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > > > > degrees > > > > nframes: 1 > > > > PhEncDir: UNKNOWN > > > > ras xform present > > > > xform info: x_r = 0.0000, y_r = 0.0000, z_r = 1.0000, c_r = > > > -1.5339 > > > > : x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = > > > 11.5254 > > > > : x_s = 0.0000, y_s = 1.0000, z_s = 0.0000, c_s = > > > -19.3390 > > > > > > > > talairach xfm : > > > > Orientation : PSR > > > > Primary Slice Direction: sagittal > > > > > > > > voxel to ras transform: > > > > 0.0000 0.0000 1.0000 -89.5339 > > > > -1.0000 0.0000 0.0000 139.5254 > > > > 0.0000 1.0000 0.0000 -147.3390 > > > > 0.0000 0.0000 0.0000 1.0000 > > > > > > > > voxel-to-ras determinant -1 > > > > > > > > ras to voxel transform: > > > > -0.0000 -1.0000 -0.0000 139.5254 > > > > -0.0000 -0.0000 1.0000 147.3390 > > > > 1.0000 0.0000 0.0000 89.5339 > > > > 0.0000 0.0000 0.0000 1.0000 > > > > > > > > > > > > > > > > > > > > Selon Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: > > > > > > > > > Hi Irene, > > > > > > > > > > since those images are not from the longitudinal runs, it really is a > > > > > cross sectional question: > > > > > > > > > > You have two images and the raw average look both similarly noisy, but > > > > > the orig (which is the first image in the recon-all stream) is smoother > > > > > for one than the other. > > > > > > > > > > That means that the conform step (that interpolates the isotropic orig > > > > > from the rawavg) introduces the different smoothing. Not sure why it is > > > > > different. > > > > > You can check (with mri_info) the voxel sizes of your rawavg and the RAS > > > > > coordinates. If they are the same, smoothing should also be the same. > > > > > > > > > > Best, Martin > > > > > > > > > > On Thu, 2011-11-03 at 17:48 +0100, Irene Altarelli wrote: > > > > > > Dear Martin, > > > > > > > > > > > > thanks for your quick reply. > > > > > > > > > > > > I am using version 5.1. I only have two timepoints per subject and I > > > > > > took the snapshots from the independent runs. What bothers me is that > > > > > > the difference is not present in the 001.mgz images, but seems to > > > appear > > > > > > later in the workflow. > > > > > > > > > > > > Thanks again, > > > > > > Irene > > > > > > > > > > > > Le jeudi 03 novembre 2011 Ãƒ 10:40 -0400, Martin Reuter a ÃƒÂ©crit : > > > > > > > Hi Irene, > > > > > > > > > > > > > > both images should be smoothed the same. You only have two time > > > points > > > > > > > in each subject? Which FreeSurfer version are you using? And these > > > > > > > images are from the *.long.base directories (or are they from the > > > > > > > independent runs)? > > > > > > > > > > > > > > -Martin > > > > > > > > > > > > > > On Thu, 2011-11-03 at 15:20 +0100, Irene Altarelli wrote: > > > > > > > > Dear Fs experts, > > > > > > > > > > > > > > > > I am running a longitudinal dataset through the longitudinal > > > pipeline, > > > > > > > > and noticed that for one subject, although we kept everything the > > > same > > > > > > > > (sequence, coil etc) the two timepoints' brainmasks look different: > > > > > > > > timepoint one (in the attached snapshot, gs_tp1) looks as if it has > > > > > been > > > > > > > > smoothed, compared to timepoint two (gs_tp2). I have checked some > > > other > > > > > > > > images from this subject, and the same seems to occur for orig.mgz, > > > but > > > > > > > > not for rawavg.mgz. > > > > > > > > > > > > > > > > Any idea on what could be causing the difference would be greatly > > > > > > > > appreciated. > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > Irene > > > > > > > > _______________________________________________ > > > > > > > > Freesurfer mailing list > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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Re: [Freesurfer] mris_anatomical stats different thickness files
by Douglas N Greve 07 Nov '11

07 Nov '11

krista kelly wrote: > Thanks Doug, but would mris_fwhm still be useful if I've already added > the -qcache command while running recon all? I have smoothed files in > my subjects' surf folders (i.e. lh.area.fwhm15.fsaverage.mgh). I want > to extract the smoothed cortical thickness and surface area values for > my subjects but am not exactly sure which commands to use. If you are going to use lh.thickness and your want it to be smoothed, then you will need to smooth it. Pass the smoothed thickness as input to mris_anatomical_stats. > > Also, I know that I don't really need to use a smoothing kernel if I'm > looking for cortical thickness within certain ROIs (presumably because > I'm getting the average), but is this also ok for surface area data? I > only ask because I'm not getting an average surface area like I am > with cortical thickness, it's the total surface area. So would > smoothing be something that I should do for surface area? For individual ROI area measures, there is no need to smooth (and does not really make sense as you point out). doug > > Thanks! > > > On Mon, Oct 24, 2011 at 4:06 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > no, that would be 15 "smooth steps". If you want to smooth by > 15mm, then use mris_fwhm. > doug > > krista kelly wrote: > > Would the following code give me data smoothed with 15 fwhm > kernel? > > mris_anatomical_stats -l lh.v1.label -t lh.thickness -nsmooth > 15 -b -f BV01/stats/lh.v1_pial.stats BV01 lh pial > > > Thanks! > > > On Mon, Oct 24, 2011 at 10:40 AM, krista kelly > <krista.kelly16(a)gmail.com <mailto:krista.kelly16@gmail.com> > <mailto:krista.kelly16@gmail.com > <mailto:krista.kelly16@gmail.com>>> wrote: > > Thanks for clearing this up! It makes a lot more sense now. > > > On Mon, Oct 24, 2011 at 10:35 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > krista kelly wrote: > > I'm looking at both cortical thickness and surface area > differences between two groups. I've been using > mris_anatomical_stats to retrieve values but had a few > questions: > > 1) Do I need to do separate mris_anatomical_stats using > different thickness files (bolded below) to get > cortical > thickness and surface area measures. For example: > > cortical thickness - mris_anatomical_stats -l > lh.v1.label > -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh > surface area - mris_anatomical_stats -l lh.v1.label -t > *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh > > > Or, since the output files include all of these > measures, > is it fine to just run one of the two? > > Just run the first one. > > > 2) The output files for both analyses run above (with > different thickness files) have identical values for > everything except for tray matter volume. Using > lh.thickness file - grayvol = 8082; using lh.area > file - > grayvol = 4029. Can anyone clarify why this happens? > > It computes the gray matter volume by thickness*area. > If you > pass it "area" as the "thickness", then you are probably > getting area*area. Though I'm surprised that the > "thickness" > values are correct. > > > 3) The default surface area values are for the white > matter surface. How do I run mri_anatomical_stats > to get > the pial surface? I've tried mris_anatomical_stats -l > lh.v1.label -t *lh.area.pial *-b -f > BV01/stats/lh.v1.stats > BV01 lh but I get identical values for everything > (except > grayvol). > > Try adding "pial" to the end of the command line (and use > lh.thickness) > doug > > > Thanks! > Krista > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto: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 > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: > 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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