Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Mask in Qdec analyses
by Tate, David Franklin 30 Aug '12

30 Aug '12

I want to be able to use a mask in some of the cortical thickness studies so as to reduce the number of comparisons being conducted as well as to be more hypothesis driven. Can anyone provide some guidance on whether or not this can be accomplished? Thanks, David

1 0

crash repport automatic hippocampus segmentation failed
by Knut J Bjuland 30 Aug '12

30 Aug '12

When I run subfield segmentation for some of the subject, I get segmentation error. Is there any known workaround these problems as recon-all is ran on a cluster? I usually get this error Rasterizing Levenberg-Marquardt.../global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh: line 18: 9231 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txtfailed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txtCan I edit kvlSegmentHippocampalSubfields.sh to ensure that it does not exit the loop at line 18.Knut J

1 0

hippocampal subfield segmentation
by Carolina Valencia 30 Aug '12

30 Aug '12

Hi Freesurfer community, A quick question, how long takes to run the hippocampal subfield segmentation for a subject that has already run the typical recon-all pipeline? Thank you, -- -- *Carolina Valencia M *

1 0

A question about hippocampal subfield segmentation
by soft.join Huang 30 Aug '12

30 Aug '12

Hi, freesurfer experts, I have a question about how to convert a segmented hippocampal subfield file into a ROI. After -hippo-subfields processing using recon-all command, I have got several files named posterior_left/right_**.mgz. And the segmented volume just coverd a small area in subject's whole brain volume. Now i want to convert the segented volume into subject's whole brain volume space and I can use it as a ROI. Is there any solution to do that? Hope for the reply. Best regards, Lijie Huang

1 0

(no subject)
by Marie Schneider 30 Aug '12

30 Aug '12

Dear FreeSurfer expects, I ran a cortical thickness analysis that revealed many significant clusters, but half of them are pretty small. Is there a possibility in qdec to display only clusters with a certain clustersize on the inflated surface? Thank you very much for your help, best wishes, Marie

1 0

freeview tracula error
by Cat Chong 29 Aug '12

29 Aug '12

Dear Experts: I have worked my way through Tracula and things seem to work fine, but when I try to view my tractography outputs I get the following persistent error using freeview (copied below). I am using a Mac OS X 10.6.7. freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Could this be a similar problem as described below? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22110.html And if so, would this be a similar fix? Cheers, cat Below is the error message I get: freeview -v $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dmri/dtifit_FA.nii.gz \ > $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/lh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' \ > $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/rh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' & [1] 24711 fmris-Mac-Pro-2:8000_tracula fmri$ 2012-08-29 12:51:30.566 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.571 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.593 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.596 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.616 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.619 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.640 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.643 freeview.bin[24711:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool))

2 2

mri_watershed and other errors.
by Darren R Gitelman 29 Aug '12

29 Aug '12

Hi I am having a problem getting recon-all to finish on 1 subject. The first time I ran recon-all -all I got an mri_watershed error. (see attached log). Based on one of the posts to the list I then ran: recon-all -skullstrip -no-wsgcaatlas -s <subj id> This completed successfully. Then I ran: recon-all -autorecon2 -autorecon3 -s <subj id> This did not complete successfully with the error that it can't find the brain.mgz file. I did look at the orig.mgz and T1.mgz files and they look fine. The talairach transform I think is also fine. What do I do about this? Thanks, Darren

2 1

contrast matrix
by Meng Li 29 Aug '12

29 Aug '12

Hi Freesurfers, My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender, the contrast matrix is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 so I can get the clusters that have significant interaction. When I perform the main effect of dignosis, is the following matrix used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 (I think it regressed out the effect of genotype and gender, that is take the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5) to perform the main effect of diagnosis. Am I correct? Any help will be very appreciated. Best wishes, Meng Li

1 0

(no subject)
by Hugh Pemberton 28 Aug '12

28 Aug '12

Hi Freesurfers, Have had this error come up after recon-all for a number of subjects and was wondering if you know what the issue is..? I have attached the recon-all.log too FYI. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ MRISread(/home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix): could not open file reading input surface /home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix... No such file or directory mris_fix_topology: could not read input surface /home/hughp/freesurfer/subjects/FAC/surf/lh.qsphere.nofix No such file or directory As the error suggests cannot read lh.qsphere, there is indeed nothing at all in the surf folder. Thanks for all your help, Hugh

2 3

mri_convert feature request?
by dgw 28 Aug '12

28 Aug '12

Hi, I'm not sure if this is a bug report or a feature request. I have been using mri_convert to convert dicoms to nii.gz and mgz files, and I have noticed some discrepancies when reading the volumes in with MRIread in either matlab or octave. The volumes differ in their support of the flip angle, tr, te, and ti fields (I realize some of this may be due to file type differences). Thought the standard output of mri_convert shows the expected values. In the mgz file the TR seems to be rounded i.e. 50 instead of 50.000000745058060 in the nii.gz In the mgz file the flip angle and te are recorded FA 0.52.... while in the nii.gz it is 0 te 10.39... while in the nii.gz it is 0 The ti value appears strange to me in the mgz ti = -1 while in the nii.gz it is 0 I have generated two files using mri convert off of the same MR volume as a test case: /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/877000-000020-000003.dcm /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/volume.nii.gz /cluster/hbot/agario_p2_2/dcm/test.mgz These files were generated using /usr/local/freesurfer/stable5_1_0/ Thanks, D

3 7

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer