Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Significant cluster only shows up in the terminal but not on the template brain
by Tudor Popescu 04 Feb '14

04 Feb '14

Dear Freesurfer experts, I ran a QDEC analysis for structural data and found, after Monte-Carlo correction(a)0.05, one significant cluster, annotated as "postcentral" (see screenshot attached). The stats associated with it are displayed in the terminal, however the statistical map on the template brain is blank. Also, when I press the "Find Cluster and Go To Max" button, I receive an error that no stats can be generated for that cluster. Not sure if it's relevant, but my dependent variables of interest in this analysis were thickness and local gyrification index (lGI). It seems I'm getting the above problem only when lGI is the DV, and whether or not there is a group factor among the categorical predictors. I do have, however, lGI analyses where the significant cluster shows up fine both on the template and in the terminal window. Can anyone help? Many thanks in advance! Best wishes, Tudor

3 6

mri_segstats - Manual Parcellation
by Gonzalo Iribarne 04 Feb '14

04 Feb '14

Hello Freesurfers, I am manually parcellating a cerebellum using Freeview and would like to compare #voxels across filled-in ROIs for reliability control. When using mri_segstats, which should be my segmentation volume? I have included my parcellation volume in the --mask option to target the voxels in my ROIs. Is this necessary or can I simply define my --seg volume as the manual (M_Parc.mgz) parcellation volume? Here is my command: mri_segstats --seg mri/testM_Parc.mgz --sum stats/testM_Parc.stats --pv mri/norm.mgz --excludeid 0 --mask testM_Parc.mgz --ctab /Volumes/share/Cerebellum/CerebellumStudyLUT.txt --subject 19 Thanks in advance! -Gonzalo Iribarne

2 1

mri_vol2surf failed, segmentation error
by Qingyang Li 04 Feb '14

04 Feb '14

Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run. Thank you all in advance! Yang ------ Qingyang Li Balance and focus. On Sun, Mar 18, 2012 at 8:28 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Mailing list subscription confirmation notice for mailing list > Freesurfer > > We have received a request from 67.244.70.75 for subscription of your > email address, "congel(a)gmail.com", to the > freesurfer(a)nmr.mgh.harvard.edu mailing list. To confirm that you want > to be added to this mailing list, simply reply to this message, > keeping the Subject: header intact. Or visit this web page: > > > https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbce… > > > Or include the following line -- and only the following line -- in a > message to freesurfer-request(a)nmr.mgh.harvard.edu: > > confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > freesurfer-owner(a)nmr.mgh.harvard.edu. > > > 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. > >

4 4

Cortical parcellation: what are the black spots?
by Qingyang Li 04 Feb '14

04 Feb '14

Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks! I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything. Thanks, Yang

2 5

Thickness values
by Natasha Haris 04 Feb '14

04 Feb '14

Hello Freesurfers, Is there anyway (command, anything on QDEC) to get a list of the thickness values in the significant clusters? Specifically, is there anyway to get the actual value of the maximum thickness in the blobs (in millimeters)? Or the mean thickness of the blobs for each subject? Thanks, Natasha

2 1

Re: [Freesurfer] ERROR: dimension mismatch between y and X.
by Douglas N Greve 04 Feb '14

04 Feb '14

Well, I'm stumped as to what is causing the problem. Yes, use mri_glmfit from the command line. You can look at the FSGD examples on our wiki. That shows you how to create contrast files doug On 01/31/2014 05:02 PM, Wanda Truong wrote: > Hi Doug, > > We're using v5.1.0 and unfortunately I don't have access to other > versions installed on another computer, currently. Would you recommend > trying the command line mri_glmfit using the > lh.area.fwhm10.fsaverage.mgh file, instead? I was always a bit > confused about how to set up my contrasts, which is why I opted to use > QDEC. > > Thanks, > Wanda > > > On 31 January 2014 13:31, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > that looks like the right size. I am stumped. What version of FS > are you > using? Do you have access to other versions? > > > On 01/31/2014 02:50 PM, Wanda Truong wrote: > > This is what I get: > > [Vinas-iMac:Wanda_SFS/qdec/Untitled] vinagoghari% ls -l y.mgh > > -rw-r--r-- 1 vinagoghari staff 1055844047 30 Jan 14:54 y.mgh > > > > > > On 31 January 2014 12:41, 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: > > > > OK, it is y.mgh that is definitely wrong. Can you send me the > > result of > > ls -l y.mgh > > > > > > > > On 01/31/2014 02:37 PM, Wanda Truong wrote: > > > > Hi Doug, > > > > Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh: > > > > [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > mri_info > > lh.area.fwhm10.fsaverage.mgh > > Volume information for lh.area.fwhm10.fsaverage.mgh > > type: MGH > > dimensions: 163842 x 1 x 1 x 46 > > voxel sizes: 1.0000, 1.0000, 1.0000 > > type: FLOAT (3) > > fov: 163842.000 > > dof: 0 > > xstart: -81921.0, xend: 81921.0 > > ystart: -0.5, yend: 0.5 > > zstart: -0.5, zend: 0.5 > > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, > flip > > angle: 0.00 degrees > > nframes: 46 > > PhEncDir: UNKNOWN > > ras xform present > > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, > > c_r = 0.0000 > > : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, > > c_a = 0.0000 > > : x_s = 0.0000, y_s = -1.0000, z_s = > 0.0000, > > c_s = 0.0000 > > > > talairach xfm : > > Orientation : LIA > > Primary Slice Direction: coronal > > > > voxel to ras transform: > > -1.0000 0.0000 0.0000 81921.0000 > > 0.0000 0.0000 1.0000 -0.5000 > > 0.0000 -1.0000 0.0000 0.5000 > > 0.0000 0.0000 0.0000 1.0000 > > > > voxel-to-ras determinant -1 > > > > ras to voxel transform: > > -1.0000 0.0000 0.0000 81921.0000 > > -0.0000 -0.0000 -1.0000 0.5000 > > -0.0000 1.0000 -0.0000 0.5000 > > 0.0000 0.0000 0.0000 1.0000 > > > > [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > mri_info > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > Volume information for > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > type: MGH > > dimensions: 163842 x 1 x 1 x 1584 > > voxel sizes: 1.0000, 1.0000, 1.0000 > > type: FLOAT (3) > > fov: 163842.000 > > dof: 0 > > xstart: -81921.0, xend: 81921.0 > > ystart: -0.5, yend: 0.5 > > zstart: -0.5, zend: 0.5 > > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, > flip > > angle: 0.00 degrees > > nframes: 1584 > > PhEncDir: UNKNOWN > > ras xform present > > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, > > c_r = 0.0000 > > : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, > > c_a = 0.0000 > > : x_s = 0.0000, y_s = -1.0000, z_s = > 0.0000, > > c_s = 0.0000 > > > > talairach xfm : > > Orientation : LIA > > Primary Slice Direction: coronal > > > > voxel to ras transform: > > -1.0000 0.0000 0.0000 81921.0000 > > 0.0000 0.0000 1.0000 -0.5000 > > 0.0000 -1.0000 0.0000 0.5000 > > 0.0000 0.0000 0.0000 1.0000 > > > > voxel-to-ras determinant -1 > > > > ras to voxel transform: > > -1.0000 0.0000 0.0000 81921.0000 > > -0.0000 -0.0000 -1.0000 0.5000 > > -0.0000 1.0000 -0.0000 0.5000 > > 0.0000 0.0000 0.0000 1.0000 > > > > Thank you! > > Wanda > > > > > > On 30 January 2014 15:30, 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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > I don't know, it is a bit bizarre. Can you run > mri_info on > > both > > lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send > > me the > > results? > > > > > > On 01/30/2014 05:01 PM, Wanda Truong wrote: > > > Hi Doug, > > > > > > Same thing happens with the other half. I'm wondering > > what file is > > > used for Y - is it lh.area.fwhm10.fsaverage.mgh? > and why > > does it > > have > > > an input number that is different from X, which should > > be the number > > > of subjects? > > > > > > Thanks, > > > Wanda > > > > > > > > > On 30 January 2014 14:19, 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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > That should be enough space. Can you try it > with the > > other > > half? I'm > > > thinking it might be one subject who is messing > > things up. > > > > > > On 01/30/2014 04:04 PM, Wanda Truong wrote: > > > > Hi Doug, > > > > > > > > I currently have 40.64 GB of disk space (is this > > enough)? > > > > > > > > I tried just now with half the subjects and it > > gave me the > > same > > > error. > > > > I was successful in completing a thickness > > analysis using > > this same > > > > method, the only thing difference this time is > > that I am > > trying > > > to do > > > > a surface area analysis. > > > > > > > > Wanda > > > > > > > > > > > > On 30 January 2014 13:12, 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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > > > > > > > Hi Wanda, I can see that it is failing, > I just > > can't > > see why > > > it is > > > > failing (and cannot replicate it here). Can > > you try a > > couple of > > > > things. > > > > First, make sure that the disk is not > filling up. > > Next, can > > > you try it > > > > with, say, half the subjects? Does this > always > > occur or is > > > it just > > > > recently? > > > > > > > > doug > > > > > > > > > > > > On 01/28/2014 04:36 PM, Wanda Truong wrote: > > > > > Hi Doug, > > > > > > > > > > Attached is the full error message I get, > > starting from > > > > mris_preproc. > > > > > > > > > > Thanks!! > > > > > Wanda > > > > > > > > > > > > > > > > > > > > On 28 January 2014 12:34, 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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>>>> wrote: > > > > > > > > > > > > > > > Can you send the terminal output that > > starts with > > > mris_preproc? > > > > > > > > > > On 01/28/2014 02:01 PM, Wanda > Truong wrote: > > > > > > Hi everyone, > > > > > > > > > > > > I get this error when running > surface area > > analysis > > > in QDEC: > > > > > > > > > > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] > > vinagoghari% > > > > mri_glmfit --y > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > > > --fsgd > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > > > dods --glmdir > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > --surf > > > > > > fsaverage lh --label > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > > > --C > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > > > > --C > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > > > gdfReadHeader: reading > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > > > INFO: DeMeanFlag keyword not found, > > DeMeaning will > > > NOT be > > > > done. > > > > > > Continuous Variable Means (all > subjects) > > > > > > 0 Age 40.6327 13.0176 > > > > > > 1 IntraCranialVol 1.50352e+06 187456 > > > > > > Class Means of each Continuous > Variable > > > > > > 1 GroupControl 38.8261 1480505.5707 > > <tel:1480505.5707> > > > <tel:1480505.5707 <tel:1480505.5707>> > > <tel:1480505.5707 <tel:1480505.5707> <tel:1480505.5707 > > <tel:1480505.5707>>> > > > > <tel:1480505.5707 <tel:1480505.5707> > > <tel:1480505.5707 <tel:1480505.5707>> <tel:1480505.5707 > > <tel:1480505.5707> > > > <tel:1480505.5707 <tel:1480505.5707> > <tel:1480505.5707 <tel:1480505.5707>>>>> > > > > > > 2 GroupRelative 42.2308 1523881.3029 > > > > > > INFO: gd2mtx_method is dods > > > > > > Reading source surface > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/surf/lh.white > > > > > > Number of vertices 163842 > > > > > > Number of faces 327680 > > > > > > Total area 65416.648438 > > > > > > AvgVtxArea 0.399267 > > > > > > AvgVtxDist 0.721953 > > > > > > StdVtxDist 0.195470 > > > > > > > > > > > > $Id: mri_glmfit.c,v 1.196.2.6 > > 2011/05/05 20:54:25 > > > greve Exp $ > > > > > > cwd > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS > > > > > > cmdline mri_glmfit --y > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > > > --fsgd > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > > > dods --glmdir > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > --surf > > > > > > fsaverage lh --label > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > > > --C > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > > > > --C > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > > > > > > > > > sysname Darwin > > > > > > hostname Vinas-iMac.local > > > > > > machine x86_64 > > > > > > user vinagoghari > > > > > > FixVertexAreaFlag = 1 > > > > > > UseMaskWithSmoothing 1 > > > > > > OneSampleGroupMean 0 > > > > > > y > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > > > logyflag 0 > > > > > > usedti 0 > > > > > > FSGD > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > > > labelmask > > > > > > > > > > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > > > maskinv 0 > > > > > > glmdir > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > > > IllCondOK 0 > > > > > > ReScaleX 1 > > > > > > DoFFx 0 > > > > > > Creating output directory > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > > > Loading y from > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > > > INFO: gd2mtx_method is dods > > > > > > Saving design matrix to > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > > > > > Normalized matrix condition is > 400.101 > > > > > > Matrix condition is 1e+08 > > > > > > Found 148151 points in label. > > > > > > Pruning voxels by thr: 0.000000 > > > > > > Found 148025 voxels in mask > > > > > > Saving mask to > > > > > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > > > > > Reshaping mriglm->mask... > > > > > > search space = 73649.347769 > > > > > > ERROR: dimension mismatch > between y and X. > > > > > > y has 3528 inputs, X has 49 rows. > > > > > > > > > > > > My QDEC table has 49 subjects,2 > > groups, and 4 > > variables. > > > > > > > > > > > > Many thanks, > > > > > > Wanda > > > > > > > > > > > > -- > > > > > > Wanda Truong, MSc > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@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>> <tel:617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>>>> > > > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > > <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>>>> > > > > <tel:617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > > <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>>> <tel:617-724-2358 > > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > > > <tel: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>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>> > > > <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>>> <tel:617-726-7422 > > <tel:617-726-7422> > > > > <tel:617-726-7422 <tel:617-726-7422>> > > > > <tel: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> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > > FileDrop: > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > > 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> > > > <http://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> > > > > > > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > Outgoing: > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > > _______________________________________________ > > > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@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 > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Wanda Truong, MSc > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@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>> > > > <tel: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>> <tel: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> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > FileDrop: > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > 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> > > > <http://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> > > > > Outgoing: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > _______________________________________________ > > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@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 > > > > > > > > > > > > > > > > > > > > -- > > > > Wanda Truong, MSc > > > > > > > > > > > > _______________________________________________ > > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@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>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@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> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > 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> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@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 > > > > > > > > > > > > > > > -- > > > Wanda Truong, MSc > > > > > > > > > _______________________________________________ > > > 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>> > > <mailto:Freesurfer@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>> > > <mailto:greve@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> > > Fax: 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> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > 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> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > 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>> > > <mailto:Freesurfer@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 > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > -- > > 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> > > Fax: 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > > 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> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Wanda Truong, MSc -- 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: 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/

1 0

FreeSurfer build stamps do not match
by Saurabh Thakur 04 Feb '14

04 Feb '14

Hello Everyone, I am getting error /////===================================================/// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ recon-all -s bert -all -hippo-subfields WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! INFO*: FreeSurfer build stamps do not match* *Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.2.0-20130111Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.2.0* INFO: SUBJECTS_DIR is /home/saurabh/Desktop/saurabh_freesurfer Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r-- 1 saurabh saurabh 423023 Jan 16 2013 /home/saurabh/Desktop/saurabh_freesurfer/bert/scripts/recon-all.log Linux saurabh-Dell-System-XPS-L502X 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /space/freesurfer/centos4.0_x86_64/stable #-------------------------------------------- #@# MotionCor Tue Feb 4 10:44:53 IST 2014 Found 3 runs /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/001.mgz /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/002.mgz /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/001.mgz has frames Linux saurabh-Dell-System-XPS-L502X 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Tue Feb 4 10:44:54 IST 2014 //---------------------------------------------------------------------------------------------------------------------// I am looking for solution asap. Thanks in advance. Saurabh Thakur,

2 1

tkmedit is not working
by Saurabh Thakur 04 Feb '14

04 Feb '14

Hi Everyone, Terminal output is: ///------------------------------------------------------------------------------------------------------////// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$* tkmedit* /usr/local/freesurfer/tktools*/tkmedit.bin: Command not found.* saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ *tksurfer* /usr/local/freesurfer/tktools*/tksurfer.bin: Command not found*. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ *recon-all* WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! USAGE: recon-all Required Arguments: -subjid <subjid> -<process directive> Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) . . . . ///--------------------------------------------------------------------------------------------------// can any one help me in this problem.....? Why* tkmedit *is not working. I am seriously looking for solution asap. Thanks in advance. *Saurabh *

3 6

Re: [Freesurfer] Installation error
by Saurabh Thakur 04 Feb '14

04 Feb '14

Hi, I am using laptop with 8Gb RAM, i7 Core processor, and enough HDD.... still i m getting same erro ( */usr/local/freesurfer/tktools/tkmedit.bin: Command not found*. ) because i m working on laptop...? or "recon-all --help " is working but *tkmedit is not working* Hope to get response asap. Thanks in advance. Saurabh Thakur, On Tue, Feb 4, 2014 at 2:09 PM, Markus Gschwind <markus.gschwind(a)gmail.com>wrote: > Hi Saurabh, > > I recently installed FS un ubuntu 12.04, and it was not difficult. > > I would recommend that you again download the file from here > http://surfer.nmr.mgh.harvard.edu/fswiki/Download (I took the Centos4 > file) > > to make sure that it is complete. > > Than you "untar" the file at any given place (most people recomment > /usr/local/ but you need to do it in "sudo" mode). > > Then make sure that you put the license file at the right place ( > http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) > > and adapt the configuration file ( > http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration) > > I used bash and it worked well. > > Take care that you have writing permission on the folders you want to use > ($SUBJECT_DIR). > For that reason I copied the folder "bert" to my home folder in order to > be able to run the installation test as recommended here: > http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer > > Hope that helps! > Cheers, > Markus > > 2014-02-04 Saurabh Thakur <srbhthkr(a)gmail.com>: > >> Hello everyone, >> >> Can u anyone help me in simplest and best way to install freesurfer on >> >> *i m not able to run command : * >> >> >> >> *1. tkmedit 2. tksurfer.System specification: * >> >> Dell laptop >> Ubuntu 12.04 LTS >> RAM 8Gb >> Graphics cards: Nvidia cards 1 Gb >> >> Thanks in advance. >> >> Saurabh Thakur, >> >> >> >> >> _______________________________________________ >> 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. >> >> >

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Join my network on LinkedIn
by Ting Xu via LinkedIn 04 Feb '14

04 Feb '14

LinkedIn ------------ Ting Xu requested to add you as a connection on LinkedIn: ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accept invitation from Ting Xu http://www.linkedin.com/e/-qq80um-hr8w2fp3-5t/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… View profile of Ting Xu http://www.linkedin.com/e/-qq80um-hr8w2fp3-5t/rso/321047558/rnBM/name/66471… ------------------------------------------ You are receiving Invitation emails. This email was intended for Freesurfer List. Learn why this is included: http://www.linkedin.com/e/-qq80um-hr8w2fp3-5t/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Freesurfer February 2014