Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 discussions

Re: [Freesurfer] t4_read error (fwd)
by Zhen Zonglei 19 Apr '09

19 Apr '09

Hi avi: Thanks for your response, attachments are my recon-all.logs. If you have any ideas,please let me know. Thanks again. 2009/4/17 Avi Snyder <avi(a)npg.wustl.edu> > Zonglei, > > Send the log file to > > avi(a)npg.wustl.edu > ---------------------------------------- > >Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT) > >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >To: Avi Snyder <avi(a)npg.wustl.edu> > >cc: nicks(a)nmr.mgh.harvard.edu > > > >do you want to contact him directly? > > > >On Fri, 17 Apr 2009, Avi Snyder wrote: > > > >> Most likely the MPRAGE->atlas computation aborted without creating > >> the relevant t4 file (ASCII representation of the affine transform). > >> This could occur if the images were somehow corrupted. > >> > >> Alternatively, the t4 file is present but a recent OS upgrade has caused > >> the previously compiled t4_read FORTRAN function to bomb. I have seen > this case > >> once before and have therefore created an all-C t4 i/o module. > >> > >> We can distinguish these cases by asking if you got a core dump, of if > >> a t4 file is still present. The complete tal transform log file would > >> be diagnostically very helpful. > >> > >> Avi > >> ------------------------------------------ > >>> Date: Fri, 17 Apr 2009 07:58:36 -0400 (EDT) > >>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >>> To: Avi Snyder <avi(a)npg.wustl.edu> > >>> cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > >>> Subject: [Freesurfer] t4_read error (fwd) > >>> > >>> Hi Avi, > >>> > >>> do you know what this message means? > >>> > >>> thanks > >>> Bruce > >>> > >>> ---------- Forwarded message ---------- > >>> Date: Fri, 17 Apr 2009 19:32:05 +0800 > >>> From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > >>> To: freesurfer(a)nmr.mgh.harvard.edu > >>> Subject: [Freesurfer] t4_read error > >>> > >>> Dear all: > >>> Recon-all has finished without error in my reconstruction. However, > when I > >>> checked recon-all.log, I found three was a error “t4_read: > >>> talsrcimg_to_711-2C_as_mni_average_305_t4 read error”. > >>> > >>> What’s this error mean? Does it have some effects on my reconstruction? > >>> > >>> Thanks > >>> > >>> -- > >>> Zonglei Zhen, PhD > >>> Assistant Professor of Cognitive Neuroscience > >>> BNU Imaging Center for Brain Research, State Key Laboratory of > Cognitive > >>> Neuroscience and Learning, P.R. China > > -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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t4_read error
by Zhen Zonglei 17 Apr '09

17 Apr '09

Dear all: Recon-all has finished without error in my reconstruction. However, when I checked recon-all.log, I found three was a error “t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error”. What’s this error mean? Does it have some effects on my reconstruction? Thanks -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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Extracting Thickness Vertex Values
by Jeff Sadino 16 Apr '09

16 Apr '09

Hello all again, I am displaying the sig.mgh file after running mris_glm. I can also see the fsgdf scatterplot when clicking on a vertex. What I would like is to be able to copy the thickness values for each subject in the group for the vertex I clicked on to an ascii/matlab/excel file. Otherwise, I'll use the mris_convert command on each subject to make an ascii file. As always, thanks for your expert help! Jeff Sadino _________________________________________________________________ Windows Live™: Life without walls. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_allup_1b_explore_042009

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dicom convert
by Gabriel Go.Es. 16 Apr '09

16 Apr '09

Dear colleages, I am trying to convert my dicom files to .mgz from Freesurfer (release 4.2) by using the mri_convert command, but it provides me the following error: [root@localhost ~]$ cd /root/trabajo/freesurfer/subjects/mci_001/mri [root@localhost mri]$ mri_convert -it dicom -ot mgz orig/001*.dcm 001.mgz mri_convert -it dicom -ot mgz orig/001088.dcm orig/001089.dcm orig/001090.dcm orig/001091.dcm orig/001092.dcm orig/001093.dcm orig/001094.dcm orig/001095.dcm orig/001096.dcm orig/001097.dcm orig/001098.dcm orig/001099.dcm orig/001100.dcm orig/001101.dcm orig/001102.dcm orig/001103.dcm orig/001104.dcm orig/001105.dcm orig/001106.dcm orig/001107.dcm orig/001108.dcm orig/001109.dcm orig/001110.dcm orig/001111.dcm orig/001112.dcm orig/001113.dcm orig/001114.dcm orig/001115.dcm orig/001116.dcm orig/001117.dcm orig/001118.dcm orig/001119.dcm orig/001120.dcm orig/001121.dcm orig/001122.dcm orig/001123.dcm orig/001124.dcm orig/001125.dcm orig/001126.dcm orig/001127.dcm orig/001128.dcm orig/001129.dcm orig/001130.dcm orig/001131.dcm orig/001132.dcm orig/001133.dcm orig/001134.dcm orig/001135.dcm orig/001136.dcm orig/001137.dcm orig/001138.dcm orig/001139.dcm orig/001140.dcm orig/001141.dcm orig/001142.dcm orig/001143.dcm orig/001144.dcm orig/001145.dcm orig/001146.dcm orig/001147.dcm orig/001148.dcm orig/001149.dcm orig/001150.dcm orig/001151.dcm orig/001152.dcm orig/001153.dcm orig/001154.dcm orig/001155.dcm orig/001156.dcm orig/001157.dcm orig/001158.dcm orig/001159.dcm orig/001160.dcm orig/001161.dcm orig/001162.dcm orig/001163.dcm orig/001164.dcm orig/001165.dcm orig/001166.dcm orig/001167.dcm orig/001168.dcm orig/001169.dcm orig/001170.dcm orig/001171.dcm orig/001172.dcm orig/001173.dcm orig/001174.dcm orig/001175.dcm orig/001176.dcm orig/001177.dcm orig/001178.dcm orig/001179.dcm orig/001180.dcm orig/001181.dcm orig/001182.dcm orig/001183.dcm orig/001184.dcm orig/001185.dcm orig/001186.dcm orig/001187.dcm orig/001188.dcm orig/001189.dcm orig/001190.dcm orig/001191.dcm orig/001192.dcm orig/001193.dcm orig/001194.dcm orig/001195.dcm orig/001196.dcm orig/001197.dcm orig/001198.dcm orig/001199.dcm orig/001200.dcm orig/001201.dcm orig/001202.dcm orig/001203.dcm orig/001204.dcm orig/001205.dcm orig/001206.dcm orig/001207.dcm orig/001208.dcm orig/001209.dcm orig/001210.dcm orig/001211.dcm orig/001212.dcm orig/001213.dcm orig/001214.dcm orig/001215.dcm orig/001216.dcm orig/001217.dcm orig/001218.dcm orig/001219.dcm orig/001220.dcm orig/001221.dcm orig/001222.dcm 001.mgz mri_convert: extra arguments ("orig/001090.dcm" and following) Could anybody help me with this problem? Thanks in advance, Gabriel _________________________________________________________________ ¿Quieres que tus hijos naveguen seguros? Aprende aquí cómo con Protección Infantil http://www.protegeatushijos.com

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freesurfer vs manual tracing
by Nicolas Cherbuin 16 Apr '09

16 Apr '09

Dear All, A paper comparing freesurfer hippocampal segmentation to manual tracing in a large middle-aged population was published today in PLOSONE and may be of interest to this list. Regards, Nic http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.00052 65 In Vivo Hippocampal Measurement and Memory: A Comparison of Manual Tracing and Automated Segmentation in a Large Community-Based Sample

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mrI_watershed volume segmentation
by slew＠nmr.mgh.harvard.edu 16 Apr '09

16 Apr '09

Hi, I used mri_watershed to get volume segmenstation with -LABEL option. mri_watershed -atlas -LABEL $SUBJECTS_DIR/test/mri/T1.mgz $SUBJECTS_DIR/test/tmp/ What coordinate system is used for the segmented volume ? The coordinate seems a lot different from that of the surface extraction with SRAS. Is RAS coordinate used for the volume segmentation? Is there a way to transform the segmented volume to SRAS ? Thanks, Seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422

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Handling non 1x1x1 voxel size data
by Barkay, Gavriel 16 Apr '09

16 Apr '09

Hi, Apologies if this question is too trivial, or it has already been answered before, but I was unable to figure this out by myself. I have volumes with voxel size 1x1x1.2mm. I was wondering what would be the best way to handle them- Run- mri_convert --confrom ? or- mri_convert --conform_min ? or run the recon-all pipeline on the data with the current voxel size ? or maybe something else? Thanks, Gabi ___ Gavriel Barkay M.D. M.Sc.

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Re: [Freesurfer] Issues with skull stripping
by Bruce Fischl 15 Apr '09

15 Apr '09

Can you send us the 1mm data so we can take a look? Bruce On Wed, 15 Apr 2009, Falk Lüsebrink wrote: > Hi Freesurfers, > > > > Im currently working on four different subjects and Im having problems > with the skull stripping for three of them. The four subjects Im trying to > process are: > > > > 1) 0.6mm iso voxel size, being the same subject as 4) > > 2) 0.5mm iso voxel size > > 3) 0.8mm iso voxel size > > 4) 1mm iso voxel size > > > > The only subject which works nearly perfectly fine is subject 1. > > > > In case of 2 and 3 there are missing parts of the brain or even a whole > hemisphere. I tried using the wsgthresh switch following the tutorial on > the wiki. In case of subject 2 the brainmask.mgz looks fairly good while > setting the threshold to 80, but still some parts of the brain are missing > and setting the threshold to 100 or 150 doesnt change much. There is not > even more skull left. > > > > For subject 3 a threshold of 30 is sufficient and the whole brain is being > shown, though some bits of skull and dura are not removed. I got a good > result for the skull stripping with v4.0.5 by not conforming the data, but I > havent been able to get the same result with v4.3.0. > > > > In case of subject 4 autorecon1 exists with an error during the talairach > check. I tried to follow the wiki for that issue, but havent been able to > even roughly match the movable with the target. So I skipped the tal-check > running into the same problem as subject 2 and 3. > > > > The command lines I used were for subject 1 to 3 recon-all autorecon1 > hires and for subject 4 just recon-all autorecon1. I tried to use > recon-all autorecon1 cm for subject 2 and 3, as this resulted in good > skull stripping using v4.0.5. But recon-all exists with an error during > mri_watershed: GLOBAL region of the brain is empty! I get the same error > if I dont use the no-wsgcaatlas switch during recon-all skullstrip, even > if I didnt use the cm or hires switches before. > > > > As Im not able to reproduce the same results between v4.0.5 and v4.3.0, > have there been made changes to the processes of autorecon1 which I havent > read of affecting the skull stripping? And does anyone have an idea besides > manually doing the skull stripping? > > > > Thanks in advance, > > Regards, > > Falk > >

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Issues with skull stripping
by Falk Lüsebrink 15 Apr '09

15 Apr '09

Hi Freesurfers, Im currently working on four different subjects and Im having problems with the skull stripping for three of them. The four subjects Im trying to process are: 1) 0.6mm iso voxel size, being the same subject as 4) 2) 0.5mm iso voxel size 3) 0.8mm iso voxel size 4) 1mm iso voxel size The only subject which works nearly perfectly fine is subject 1. In case of 2 and 3 there are missing parts of the brain or even a whole hemisphere. I tried using the wsgthresh switch following the tutorial on the wiki. In case of subject 2 the brainmask.mgz looks fairly good while setting the threshold to 80, but still some parts of the brain are missing and setting the threshold to 100 or 150 doesnt change much. There is not even more skull left. For subject 3 a threshold of 30 is sufficient and the whole brain is being shown, though some bits of skull and dura are not removed. I got a good result for the skull stripping with v4.0.5 by not conforming the data, but I havent been able to get the same result with v4.3.0. In case of subject 4 autorecon1 exists with an error during the talairach check. I tried to follow the wiki for that issue, but havent been able to even roughly match the movable with the target. So I skipped the tal-check running into the same problem as subject 2 and 3. The command lines I used were for subject 1 to 3 recon-all autorecon1 hires and for subject 4 just recon-all autorecon1. I tried to use recon-all autorecon1 cm for subject 2 and 3, as this resulted in good skull stripping using v4.0.5. But recon-all exists with an error during mri_watershed: GLOBAL region of the brain is empty! I get the same error if I dont use the no-wsgcaatlas switch during recon-all skullstrip, even if I didnt use the cm or hires switches before. As Im not able to reproduce the same results between v4.0.5 and v4.3.0, have there been made changes to the processes of autorecon1 which I havent read of affecting the skull stripping? And does anyone have an idea besides manually doing the skull stripping? Thanks in advance, Regards, Falk

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Re: [Freesurfer] mri_ca_train parameters?
by Nick Schmansky 14 Apr '09

14 Apr '09

Jamie, The script would contains lines like this: set SUBJECTS=(subj1 subj2 subj3 subj4) set ONE_SUBJECT=(subj3) When rebuilding the atlas of 40 subjects on our cluster, where each subject gets its own node, it takes about 2 days. so on a single machine, about 80 days. Nick On Wed, 2009-04-08 at 16:32 -0500, Jamie Hanson wrote: > > so that it just runs the command locally. note that this script submits > > multiple subjects to multiple nodes, so if you have 30 subjects, and you > > dont use a cluster, it will take much much much longer to complete. > > Hi Nick- > > I am working on that script right now. One quick question about this, > is there an example of the subjects.csh file (to specify files for > training?). I understand I need to set for ONE_SUBJECT variable, but I > wasn't sure how the other SUBJECTS should be specified (and couldn't > find any other examples on-line or in my version of freesurfer). > > RE: computation load / time... It sounds like 2 days w/ multiple > nodes... We don't do any job queue / cluster batching system, so for a > single machine, what is a rough ball-park for completion time? > > Thanks much! > jamie. > > > > > > Nick > > > > > > On Tue, 2009-04-07 at 12:16 -0500, Jamie Hanson wrote: > >> Hi Freesufer folks- > >> > >> I was just about to start constructing a custom aseg atlas and I > >> wondered if there were any recommendations for any of the optional > >> flags? Any parameters yield better results (especially for specific > >> brain regions)? I was focused on improving amygdala segmentation for > >> my structural images (hence my asking). > >> > >> Best, > >> jamie. > >> > >> > >> > >> > > > > > > >

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Freesurfer April 2009