Freesurfer February 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
80 discussions

output orientation incorrect
by Leila BH 15 Feb '07

15 Feb '07

Hello, I am new freesurfer user, I need to have the labels of parcellation on analyze format. I did recon all command on my subject, I see the very beautiful parcellation on freesurfer. After reading all the question/response on the freesurfer website, I write my own txt file describing the 35 labels: I just copy paste the data obtained from the variable colortable.struct_name and colortable.table: the output of read_annotation('rh.aparc.annot'). It seems working correctly, because the mri_annotation2label creates 35 files of all the labels. To check some of them I used tkmedit chuv44 brain.mgz and I loaded one label, it seems good. Is this correct? But when I tried to export this labels to analyze format (readable with mricro for example), I use mri_label2vol: Mri_label2vol -label ./subects/chuv44/mylab/rh.superiorfrontal.label -temp $SUBJECTS_DIR/chuv44/mri/orig/chuv44.img -o ./subjects/chuv44_rh_one.img I had a warning saying that the mat file is missing, and the result orientation is not good. I then open my analyze file with v=spm_vol('chuv44.img') and copy the v.mat as the mat file freesurfer asked for: v.mat ans = -2 0 0 129 0 2 0 -129 0 0 2 -69 0 0 0 1 The command line Mri_label2vol -label ./subects/chuv44/mylab/rh.superiorfrontal.label -temp $SUBJECTS_DIR/chuv44/mri/orig/chuv44.img -o ./subjects/chuv44_rh_one.img works then correctly and write in the end: Analyze output matrix -2 0 0 129 0 2 0 -129 0 0 2 -69 0 0 0 1 --------------------- INFO: set hdr.hist.orient to -1 But when I open the output file chuv44_rh_one.img (analyze) the format is not the same as my image: the axial slice is coronal and vice versa. First question: Is the staff I did with my home-made txt labels_file is correct? And do you know what I should do to obtain my label mask in correct orientation? Thanks in advance Leila Cammoun

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Installation on sun grid
by Inge K. Amlien 15 Feb '07

15 Feb '07

Hello list, we are installing Freesurfer on a computer cluster (about 400 cpu's) running the Sun Grid Engine. As there are other applications installed on the compute nodes and space is limited, we would like to strip out any files from the Freesurfer installation not needed for processing. Is it safe to remove any files/folders other than the example subjects? Tkmedit/tksurfer? Kind regards Inge Kasbohm Amlien Department of Psychology University of Oslo

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how to read 'lh.inflated.asc' using matlab
by r.huang＠fz-juelich.de 15 Feb '07

15 Feb '07

Hello Everyone, I want to know how to load one asc file into matlab. Using mris_convert, I obtained 'rh.lh.sphere.reg.asc'. The procedure is here mris_convert rh.lh.sphere.reg rh.lh.sphere.reg.asc In matlab, when I applied fname='rh.lh.sphere.reg.asc' [S, v, f] = read_asc(fname) the following message comes out [??? Error using ==> reshape To RESHAPE the number of elements must not change. Error in ==> read_asc at 23 f = reshape(f, [5 S(3)])';] Do you know how to solve the problem? Thanks in advance rhuang

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Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 14 Feb '07

14 Feb '07

Here are the details of the acquisitions: Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix) The machine has 4 gigs of RAM. Also, AFNI is able to talairach and skull strip. Is there a way I can input the files from AFNI to Freesurfer to resume the recon-all pipeline. Nick, is there a way for me to see your reg so that I can be sure that its not my created xfm that is causing this problem. Thanks, Anil. On 2/14/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > why is the background so high? Also, what field strength was this at? > There > looks to be dielectric-like center brightening. The contrast isn't > terrible > though. > > On Wed, 14 Feb 2007, Nick > Schmansky wrote: > > > Bruce, > > > > the orig.mgz can be downloaded via the filedrop, see link in email > > below. > > > > or i have copied it to: > > > > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > > > > N. > > > > > > On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl wrote: > >> put the .mgz somewhere and I'll take a look. And make sure it's the > >> orig.mgz, which is un-normalized > >> > >> > >> On Wed, 14 Feb 2007, Nick Schmansky wrote: > >> > >>> Anil, > >>> > >>> The image has almost no contrast. I've attached a TIFF of one slice. > >>> How was this acquired? Bruce, any idea why it would be so white? > >>> > >>> Nick > >>> > >>> > >>> On Wed, 2007-02-14 at 16:10 -0500, aroy85(a)gmail.com wrote: > >>>> The following files have been uploaded to the Martinos Center > FileDrop site > >>>> by Anil Roy for you to download: > >>>> > >>>> (1) orig.mgz > >>>> > >>>> > >>>> > >>>> These files will expire in 30 days. > >>>> > >>>> To view or download these files, go in your web browser to: > >>>> > >>>> > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > >>>> > >>>> DO NOT SHARE this web address with anyone else. It is your personal > access key to the files. > >>>> > >>>> Overall Comment about files from Anil Roy: > >>>> > >>>> Hi, > >>>> > >>>> Attached is the orig.mgz file for the subject that quits at the > watershed step. > >>>> > >>>> Thanks, > >>>> > >>>> Anil. > >>>> > >>>> > >>> > >> > >> > > > > > > >

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Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 14 Feb '07

14 Feb '07

Nick, The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform you that I converted the orginal 120 slices into afni brik format (afni was able to read them) and then used mri_convert to convert the BRIK to cor. Freesurfer then used this cor to run the recon-all pipeline. The original files could not be read by Freesurfer which is why I did that. Also, this may be obvious to you but cannot the contrast be simply changed by Freesurfer. In tkmedit, the brightness and contrast can be adjusted so isn't there a way that recon-all can use this change while running the brain. Thanks - Anil On 2/14/07, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Anil, > > The image has almost no contrast. I've attached a TIFF of one slice. > How was this acquired? Bruce, any idea why it would be so white? > > Nick > > > On Wed, 2007-02-14 at 16:10 -0500, aroy85(a)gmail.com wrote: > > The following files have been uploaded to the Martinos Center FileDrop > site > > by Anil Roy for you to download: > > > > (1) orig.mgz > > > > > > > > These files will expire in 30 days. > > > > To view or download these files, go in your web browser to: > > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > > > > DO NOT SHARE this web address with anyone else. It is your personal > access key to the files. > > > > Overall Comment about files from Anil Roy: > > > > Hi, > > > > Attached is the orig.mgz file for the subject that quits at the > watershed step. > > > > Thanks, > > > > Anil. > > > > > >

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longitudinal analysis - error
by Chacko Cherian 14 Feb '07

14 Feb '07

Hello all, This is an error I got while running the longitudinal analysis on one of our subjects.It didnt create the filled.mgz volume and so the surfaces weren't created. #@# Fill Tue Feb 13 20:59:04 MST 2007 /ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... fill: could not scan threshold from 'norm.mgz'Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Tue Feb 13 20:59:04 MST 2007 THanks in advance Chacko. ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/

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recon-all error
by Anil Roy 14 Feb '07

14 Feb '07

Hello all, I have some raw data and I'm not sure of the format. Its definitely not dicom. I ran recon-all on these files but I get an error saying it can't read the files. I have posted the output below. I tried to convert the files to afni format (BRIK + HEAD), and tried recon-all again. It ran for a while but gave an error that I've attached to a text file. Can someone please tell me how I can get Freesurfer to read these files. I can also upload the raw files if you'd like to take a look at them. Thanks a lot - Anil. [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001 -sd /root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200

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64bit centos utilities: mris_wm_volume & mris_volume
by Juranek, Jenifer 14 Feb '07

14 Feb '07

Recently (7 Feb 2007) mris_wm_volume for 32bit centos was posted in /pub/dist. Is there any possibility of posting 64bit centos versions of mris_wm_volume & mris_volume? I'm running Freesurfer 3.0.4 Many Thanks, Jenifer

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pial editing
by Derin Cobia 14 Feb '07

14 Feb '07

I have a question regarding editing the pial surface. Many times it includes bright spots, such as fat or vessels. Should I be editing this out? I'm pretty clear on getting rid of included dura, but if I spent the time to edit out every little bright spot, it would be pretty time intensive. Would leaving these little "extras" skew my data? Is there some balance I can strike when editing? Thanks! -Derin

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WM vol
by Nurunisa Neyzi 14 Feb '07

14 Feb '07

Hi, when I use mri_anatomical stats - I get a total WM value 503450 for left and right hemispheres that's the same number in the stats file in the stats folder. but when I use mris_wm_volume - I get 174896 and 178464 which one is the accurate one? also, is the GM volume I get from mris_anatomical_stats accurate? thanks, n. 174896 17464

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Freesurfer February 2007