Freesurfer

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30132 discussions

Longitudinal Processing Error
by Jonathan Holt 01 Jul '13

01 Jul '13

Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon

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Re: [Freesurfer] Problem with FS-FAST, mkcontrast (Douglas N Greve)
by O'Shea,Andrew 01 Jul '13

01 Jul '13

I have matlab installed. I have the following lines in my ~/matlab/startup.m file %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% Is there a way check to see if the path is set correctly? Message: 9 Date: Mon, 01 Jul 2013 09:46:39 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Problem with FS-FAST, mkcontrast To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <51D1883F.5050103(a)nmr.mgh.harvard.edu<mailto:51D1883F.5050103@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed doyou have matlab installed and in your path? doug On 07/01/2013 08:55 AM, O'Shea,Andrew wrote: Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 ' I get the following output error: " phhp-jcraggs-mb:Project aoshea$ mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 INFO: Found 1 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test/pain-v-rest.mat nconds 1, wcond 1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave Mon Jul 1 08:51:02 EDT 2013 " It is not creating a .mat file in the analysis directory. Any suggestions would be greatly appreciated. Thanks! -Andrew _______________________________________________ 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 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/

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Re: [Freesurfer] Fwd: DTI questions
by Anastasia Yendiki 01 Jul '13

01 Jul '13

Hi Rotem - No problem. Were these scans by any chance acquired with a coronal slice prescription? In the axial views that you sent, the artifact that you're pointing to looks like misalignment between consecutive coronal slices, which could be due to head motion. a.y On Tue, 25 Jun 2013, Rotem Saar wrote: > Dear Anastasia, > > I tried several times to upload these images in a non-compressed way, but > they were too big and my posts were rejected, with no opportunity for any > other upload way. > Is there any other way for me to upload it so that everyone can see it ? > > Attached are the images in a non-compressed fashion. I will be very happy if > u will have a look, and post your answer to me and the list to save some > time, until I will be able to consider another way to upload them. > > I know that we should write to all the list, but at the moment if the images > are not visible this won't help - so I will really appreciate if u will have > a look but also tell me what is the best way to upload them so that all list > members will be able to see them. > > Thank u very much for your help. > > Rotem > > 2013/6/25 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Sorry, can't open the image. > > On Sun, 23 Jun 2013, Rotem Saar wrote: > > Hi there, > > Long time:). Well I wrote to the list several times > regarding high FA values > I got when performing DTI analysis. > Today we know that the problem was an additional > direction (we had 17 > directions instead of 16 - we used a Philips > scanner,1.5T). So we deleted > the additional slices and the high values indeed > disappeared, but then > another problem came up (tried several subjects so > the problem is not > specific to a subject) - > > I noticed an artifact that I can't explain - please > see the attached > pictures. > > This artifact existed even before I deleted the > additional slices, also - I > see the artifact also when loading the masked > volume...It is cyclic - run > over all slices... > > any ideas ? > > I'm using version 5.2 and I know the command lines > are correct (send it to u > in the past). > > Thanks for your help > > Rotem > > > > > 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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Pial surface consistently misplaced
by Jonathan Holt 01 Jul '13

01 Jul '13

Hi all, I'm having a bit of trouble with one particular subject for which we brains for 4-5 different time points. The pial surface is consistently misplaced in the same area, see attached main/aux volume images. I'm hesitant to manually replace the white matter myself as I fear it wouldn't be as accurate. Suggestions on other methods to fix this? The problem is always in the LH temporal right around the lateral inferior ventricle and the fusiform and other subcortical structures.

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Tracula/Config file error
by Gundran, Andrew 01 Jul '13

01 Jul '13

I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing "set: Variable name must begin with a letter" Its become very annoying.

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Re: [Freesurfer] Xhemi question
by Douglas N Greve 01 Jul '13

01 Jul '13

Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: > Hi Doug, > > We are experimenting with adding xhemi to our processing stream. Is there > is a way to QC the results at an individual subject level? > > Best, > Daria > > > Daria A. Boratyn, > Clinical Research Coordinator > MS Imaging Lab > Massachusetts General Hospital > 149 13th Street | Boston, MA 02129 > 617-726-7531 > > -- 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/

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T1-weighted anatomical
by ye tian 01 Jul '13

01 Jul '13

Dear freesurfers, My data seems not to be T1-weighted by look ( http://www.youtube.com/watch?v=W8ZFGvGvHVc) Would you please help me further identify by reading the following experimental description? Images were acquired with blood-oxygen level dependent (BOLD) imaging on a 3 T Siemens Trio Scanner (Bandettini, Wong, Hinks, Tikofsky, and Hyde, 1992). A five-minute magnetization prepared, rapid-acquisition gradient echo image (*MPRAGE*) was acquired for anatomic overlays of *functional*data and spatial normalization (T1 MN1 Template). BOLD imaging used a 33-slice whole-brain, single-shot gradient echo (GE) echo-planar (EPI) sequence (TR/TE = 2000/25 ms, FOV = 240 mm, matrix = 64 x 64, slice thickness/gap = 4/0 mm). This sequence delivers a nominal voxel resolution of 3 x 3 x 3 mm. Also, if I do *mri_info *in freesurfer for the five sequences of the data, Series Number 1: TR: 8.6msec, TE: 4.00msec, T1: -1.00msec, Flip Angle: 20.00degrees Series Number 2: TR: 2000.00msec, TE: 25.0msec, T1: -1.00msec, Flip Angle: 90.00degrees Series Number 3: TR: 2300.00msec, TE: 2.96msec; T1: 900.00msec, Flip Angle: 90.00degrees Series Number 4&5: TR: 2000.00msec, TE: 25.00msec; T1: -1.00msec, Flipe Angle: 90.00degrees Is my data NOT T1-weighted for sure? Thank you very much! Sincerely, Ye * *

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Control Point Problem
by LIOR ZWANZIGER 01 Jul '13

01 Jul '13

Hi, I have been using control points to correct excluded white matter and ran into the same problem as Peter, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-July/024771.html , in that the opposite hemisphere's boundaries recede after control points are added and then recon-alled. Has this issue been resolved in 5.2 or 5.3? Thanks, Lior Zwanziger

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Tracula/config file issue
by Gundran, Andrew 01 Jul '13

01 Jul '13

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Qdec error
by Anupa AV 01 Jul '13

01 Jul '13

Dear All, When I tried to running qdec, I'm getting the following error. qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory What is the solution for this.? Any help will be greatly appreciated.

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