Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

Error of fsaverage unknown during mri_glmfit
by newfei＠nmr.mgh.harvard.edu 13 May '10

13 May '10

Hi, I encountered the error of 'option fsaverage unknown' when running the mri_glmfit. Any idea on what I have missed during the steps leading to this? [audrey:newfeiGLM] (nmr-std-env) mri_glmfit --y lh.Vis_schiz.thickness.10.mgh --fsgd Vis_schiz.fsgd dods --C age.mtx -surf fsaverage lh --cortex --glmdir lh.Vis_schiz.glmdir gdfReadHeader: reading Vis_schiz.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 41.2941 1 PremorbidIQ 107.942 2 BDI 5.41176 Class Means of each Continuous Variable 1 Control 41.3333 113.6880 2.4000 2 Schiz 41.2632 103.4053 7.7895 INFO: gd2mtx_method is dods ERROR: Option fsaverage unknown Thanks in advance, Newfei

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Fwd: problems with tksurfer
by Krish Subramaniam 13 May '10

13 May '10

FYI.. Begin forwarded message: > From: iacono(a)nmr.mgh.harvard.edu > Date: May 13, 2010 3:11:09 PM EDT > To: "Krish Subramaniam" <krish(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] problems with tksurfer > > Thanks Krish! > you solved my problem. > I mean, I made just a small error in typing the SUBJECT_DIR and with > ls > $SUBECTS_DIR I realized it! > Sorry for the trivial question and thanks for your help! > Maria > > >> Hi Maria >> >> The SUBJECTS_DIR is one directory above the my_subj_name. Sorry if >> this is a trivial point, but worth a check. >> >> can you give me the output of following commands >> >> echo $SUBJECTS_DIR >> ls $SUBJECTS_DIR >> >> On May 12, 2010, at 7:03 PM, iacono(a)nmr.mgh.harvard.edu wrote: >> >>> Hi all! >>> I have some problems to visualize surfaces by tksurfer. When I try >>> to load >>> a surface with the command tksurfer my_subj_name lh inflated I >>> receive the >>> following error: >>> ERROR: could not read header info from T1 or orig in >>> homes/..../my_subj_name/mri >>> The SUBJECTS_DIR is the correct one and in my mri folder there are >>> both >>> T1.mgz and orig.mgz. >>> Any suggestion? Could the headers of those files be corrupted? How >>> can I >>> check it? >>> Thanks in advance for any help! >>> Maria >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> > >

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problems with tksurfer
by iacono＠nmr.mgh.harvard.edu 13 May '10

13 May '10

Hi all! I have some problems to visualize surfaces by tksurfer. When I try to load a surface with the command tksurfer my_subj_name lh inflated I receive the following error: ERROR: could not read header info from T1 or orig in homes/..../my_subj_name/mri The SUBJECTS_DIR is the correct one and in my mri folder there are both T1.mgz and orig.mgz. Any suggestion? Could the headers of those files be corrupted? How can I check it? Thanks in advance for any help! Maria

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talairach to native space
by Tina Jeon 13 May '10

13 May '10

Hello freesurfers, I am trying to align my T1W image in native space to the surface files (?h.pial, ?h.white, ?h.inflated, ?h.base) but it seems that they do no align perfectly. I thought the labeling information is in native space? However this does not seem to be the case because in the ascii files for the surfaces we found -120 in the coordinates but native space is [0,240] (i.e., without negatives). Is using tkregister2 the solution? Or using an affine registration matrix to transform the coordinates? Thanks in advance. Your help would be greatly appreciated. Tina Jeon

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Re: [Freesurfer] Subcortical segmentation
by Allison Stevens 13 May '10

13 May '10

If you want to use the subcortical volume measures, you defnitely want to make sure they are accurately following the intensity boundaries of the structures. That wiki page is a little misleading in that sense (I'll work on updating it). When I'm checking a recon for the other potential problems listed there (skull strip issues, wm segmentation problems, pial edits, etc.), that's when I also check the accuracy of the aseg (although I rarely find any problems). Allison On Thu, 13 May 2010, Martin Ystad wrote: > Ok, but since it does not say to routinely check it, my guess is that people > who run hundreds of subjects through FreeSurfer (myself included) probably > don't, which is fine since manual edits are discouraged anyway? Would another > way of doing it be to check for outliers in the volumes produced by the > subcortical segmentation procedure, and take a closer look at subjects that > appear there? > > (There is no particular structure that appears to be inaccurate. I was just > curious, as I'm compiling my thesis where I mention FreeSurfer-technology as > a possible future clinical tool :) > Thanks, > Martin > > Allison Stevens wrote: >> It should probably say to check it and make sure it is accurate although >> you are right that we generally advise against manually editing it >> (especially without trying automatic methods first). If there is a >> structure you are interested in that is quite inaccurate let us know. >> >> On May 13, 2010, at 8:23 AM, Martin Ystad <martin.ystad(a)biomed.uib.no> >> wrote: >> >> >> > Maybe I've misunderstood. In >> > http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction , >> > after autorecon2 it says to check white and pial surfaces before running >> > autorecon3. The linked tutorials on how to do WM, Pial and Final >> > surfaces edits, does not mention checking the aseg as far as I can see. >> > Also, to express myself more clearly: I'm thinking of the labeling of >> > the subcortical structures (thalamus, putamen, etc.). Is there something >> > I'm missing here? >> > - Martin >> > >> > Allison Stevens wrote: >> > >> > > It should be part of the workflow. Can you show me where it was not >> > > listed? >> > > >> > > On May 13, 2010, at 7:58 AM, Martin Ystad <martin.ystad(a)biomed.uib.no> >> > > wrote: >> > > >> > > >> > > >> > > > Hi, I noticed that routinely checking the subcortical segmentation >> > > > (aseg.mgz) is not part of the Recommended Reconstruction Work Flow. >> > > > Is this because the subcortical segmentation is highly accurate, or >> > > > because manual intervention in the aseg is not recommended anyway? >> > > > >> > > > Thanks, >> > > > Martin Ystad >> > > > PhD-student >> > > > University of Bergen, Norway >>>>> _______________________________________________ >> > > > 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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qdec syntax question
by ridatta＠mail.med.upenn.edu 13 May '10

13 May '10

Hello All, I have a very simple qdec question. I have three groups (relatively age and sex matched), each grp has 8 subjects. I have created a qdec.table.dat file with contents as follows SUBJECT_DIR /jet/rito/freesurfer_data/ fsid gender age diagnosis 01 Female 40 Group1 02 Female 32 Group1 03 Female 41 Group1 04 Female 33 Group1 05 Female 36 Group1 06 Female 37 Group1 07 Male 49 Group1 08 Male 46 Group1 09 Male 37 Group2 10 Female 38 Group2 11 Male 38 Group2 12 Female 32 Group2 13 Female 32 Group2 14 Female 45 Group2 15 Female 31 Group2 16 Female 45 Group2 17 Female 32 Group3 18 Female 40 Group3 19 Male 45 Group3 20 Female 32 Group3 21 Male 31 Group3 22 Female 30 Group3 23 Female 32 Group3 24 Female 36 Group3 I have also created two discrete factors.level files, gender.level Female Male diagnosis.level Group1 Group2 Group3 When I try to load the qdec.table.dat file, I get an error - /jet/rito/freesurfer_data/qdec$ Loading data table qdec.table.dat... Setting SUBJECTS_DIR to /jet/rito/freesurfer_data/ Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 24 Data table qdec.table.dat loaded. SUBJECTS_DIR is '/jet/rito/freesurfer_data/' sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '2' in SUBJECTS_DIR sh: Syntax error: Bad fd number etc Can you tell me what am I doing wrong ? Thanks Ri

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freesurfer recon-all running in a few seconds without error?
by Jason Connolly 13 May '10

13 May '10

Dear freesurfer experts: Recon-all is running in a few seconds (obvious error). I am getting the following screen output on Linux, when I run recon-all: recon-all -i /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s arlene -force INFO: /usr/local/freesurfer/subjects/arlene exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 lab root 59398 May 13 15:07 /usr/local/freesurfer/subjects/arlene/scripts/recon-all.log Linux ionimagelab1 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/arlene mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998356, -0.0445698, 0.0360538) j_ras = (0.0395912, -0.0812138, 0.99591) k_ras = (0.0414595, -0.9957, -0.0828448) writing to /usr/local/freesurfer/subjects/arlene/mri/orig/001.mgz... #------------------------------------------ recon-all finished without error at Thu May 13 15:08:08 BST 2010 The TR, flig angle etc. are all 0.00 ... Do you have any ideas? Many thanks, Jason.

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Subcortical segmentation
by Martin Ystad 13 May '10

13 May '10

Hi, I noticed that routinely checking the subcortical segmentation (aseg.mgz) is not part of the Recommended Reconstruction Work Flow. Is this because the subcortical segmentation is highly accurate, or because manual intervention in the aseg is not recommended anyway? Thanks, Martin Ystad PhD-student University of Bergen, Norway

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Label two volume conversion
by Martin Kavec 13 May '10

13 May '10

Hi, using tksurfer, I have created labels corresponding to significantly thinner cortex between two groups of my subjects. After that I converted the labels to volumes (mri_label2vol), which I would like to use for further analysis. However, the volumes cover only the interface between gray and white matter, while I would need the entire cortex. Is there any way to achieve this? Thanks in advance, Martin

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Re: [Freesurfer] Number of Voxels different between wmparc.mgz and wmparc.stats
by Sita Kakunoori 12 May '10

12 May '10

Hi Christopher, the values in wmparc.stats are computed with partial volume correction. Sita. On Wed, 12 May 2010, Christopher Coello wrote: > Hello, > > > > After segmenting using recon-all all, I want to look at how much voxels > there is in each segmented structure. > > I did the following procedure : I opened the wmparc.mgz volume with 3DSlicer > as a label volume and computed the LabelStatistics. > > For the label 1005 (ctx-lh-cuneus), the count value is 3133. But in the > wmparc.stats, the numVox in front of the label 1005 is 2729. This difference > exists for many of the segmented structures. > > To double check, I also opened the wmparc.mgz with Matlab to count the > number of voxels labeled 1005 in the volume, and I do find 3133. > > Am I comparing 2 different values ? Or is there a bug in the writing of the > wmparc.stats ? > > > > Best regards, > > > > Christopher Coello, > > Postdoctoral Research Fellow > > Center for Diagnostic Imaging, > > Akershus University Hospital, > > Sykehusveien 25, 1478 Lørenskøg > > tel : +4745154516 > > e-mail : christopher.coello(a)medisin.uio.no > > > >

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Freesurfer May 2010