Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

error with .lta files in longitudinal
by Justin McKee 12 Oct '15

12 Oct '15

Hi, I’ve not idea why a few of my longitudinal runs have started to fail. It’s saying there’s a problem with the .lta files, >From “bugr” script FREESURFER_HOME: /opt/fmrib/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 I ‘ve lost the exact command line but it would have been recon-all –long ACT_364_12M ACT_364_3scan_base -all The error message is mri_convert -at /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta -odt uchar -rt cubic /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M.long.ACT_364_3scan_base/mri/orig.mgz mri_convert -at /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta -odt uchar -rt cubic /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M.long.ACT_364_3scan_base/mri/orig.mgz ltaReadFile(/home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: Reading transformation from file /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta Linux jalapeno12.fmrib.ox.ac.uk 2.6.32-504.12.2.el6.x86_64 #1 SMP Wed Mar 11 22:03:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ACT_364_12M.long.ACT_364_3scan_base exited with ERRORS at Mon Oct 12 18:16:19 BST 2015 I’m a bit confused because /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ Has a full complement of.lta files including the one mentioned in the error message.. Obviously it’s taken a while to get to this stage so I’m loathe to re-run the –base and –long again, as I had made extensive edits to the ACT_364_3scan_base brain mask file and ran autorecon-pial and don’t want to loose those if possible, or indeed do them again and get the same mistake at this stage. Have attached the recon-all.log file Any help gratefully received! Cheers Justin Dr Justin McKee Clinical Research Fellow in Multiple Sclerosis Nuffield Department of Clinical Neuroscience University of Oxford

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high resolution data using recon-all
by Yun Wang 12 Oct '15

12 Oct '15

Hi All, I have 7T high resolution data 0.625mm. Is it appropriate to process the data using recon-all ? If not, any idea? Thanks! Yun Wang

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Error: cannot determine file type
by will brown 12 Oct '15

12 Oct '15

Hi all, Am receiving the below error, I haven't used this scan before but have never had issues with .dcm. Sorry I'm not sure what sort of scanner they are from. Any help would be appreciated. Cheers, Will /usr/local/freesurfer/subjects/YU mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm /usr/local/freesurfer/subjects/YU/mri/orig/001.mgz mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm /usr/local/freesurfer/subjects/YU/mri/orig/001.mgz ERROR: cannot determine file type for /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm Linux localhost.localdomain 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s YU exited with ERRORS at Mon Oct 12 21:21:24 NZDT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] longitudinal stream: adding a time point
by Martin Reuter 11 Oct '15

11 Oct '15

Hi Ruthi, that is possible in several ways. The question is what images do you want to map and for what purposes. For easy transfer of control points or edits, it should be OK, or external data that you created and want to take along (fMRI or other images). But if you plan to map images that are part of the stream and then further process it, that may be problematic (again because of potential biases that may sneak in). So to go from old base to new you can a) register the base images (e.g. norm.mgz) and then use the transform to map stuff (I think this would do the trick: mri_robust_register --mov <oldnorm.mgz> --dst <newnorm.mgz> --lta old2new.lta --mapmov old2new.mgz --sat 6 you can then use mri_convert or vol2vol to map stuff using the lta (make sure to use nearest neighbor interpolation for label maps and cubic interpolation for images). In mri_convert -rt cubic or -rt nearest b) you can concatenate the existing transform from a cross sectional to the old base (actually the inverse) with the new transform from that time point to the new base. The problem here is (although it should not matter much) that you again need to select a specific time point and that is again a potential source of bias. Also if you accidentally select a time point with motion artifacts or other problems this could be unstable. So I recommend option a). Best Martin > On Oct 11, 2015, at 6:20 AM, Adam, Ruth <Ruth.Adam(a)med.uni-muenchen.de> wrote: > > Thank you Martin! > In that case, is there an easy way to register volumes marked on the old 2 time-points base to a new 3 time-points base? > Have a nice week. > > Best, > ruthi > > Message: 3 > Date: Thu, 8 Oct 2015 20:18:47 +0200 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] longitudinal stream: adding a time point > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <4599EF79-C8D8-4448-ADE3-3941CAA18D41(a)nmr.mgh.harvard.edu <mailto:4599EF79-C8D8-4448-ADE3-3941CAA18D41@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="us-ascii" > > Hi Ruthi, > > it is possible to add time points retrospectively without re-creating the base. However this will likely induce a processing bias, as the 3rd time point is treated differently from the first two. How big that is going to be nobody knows (it depends on your data and on the number of time points). The more time points are in the base, the less of a problem it should be, but with only 2, adding a 3rd may not be good. > > Here is how you can do it > recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all > but I recommend against it. If you do, you definitely need to describe this in the publication as it is not the standard procedure. You should also run several cases (maybe ones that did not need edits) separately with 3 time points in the base and test for differences. > > The re-creation of the base is the biggest problem in unbiased longitudinal processing, but necessary to ensure all time points undergo exactly the same treatment. > > Best, Martin > >> On Oct 8, 2015, at 4:40 PM, Adam, Ruth <Ruth.Adam(a)med.uni-muenchen.de <mailto:Ruth.Adam@med.uni-muenchen.de>> wrote: >> >> Dear all, >> >> We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. >> Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points) and instead register the third time point to the pre-existing template. >> What is the best way to do so? Is there a way to force recon-all to use a specific template? >> >> Many thanks! >> >> Best, >> ruthi

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repeated measures ANOVA using the FSGD file
by pablo najt 10 Oct '15

10 Oct '15

Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand would basically be a repeated measures design. My design has 3 groups (HC, PT relatives and PT).Instead of time points of the same subject my design matrix uses each family member within a family. So I will have many subjects within family_1, same for family_2 and so on... I also want to include gender as a covariate. In short my question is:For my design in repeated measures do I need to define all my groups for each discrete variable as how we do it for glm?For example if I want to have variables GROUP + GENDER + FAMILY.Should i do it as follows?class HC_Female_Family1class PT_Female_Family1class HC_Male_Family2class HC_Female_Family2...... Many thanks,Pablo

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A potential problem in qdec
by chenhf_uestc 09 Oct '15

09 Oct '15

Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but there was an error (acctached error.png) that puzzled me for a long time. I and my colleague help me to check all the files but do not find where is the error. I performed the same analyses on other computers, there was the same error. However, if I remove the files gender.levels, group.levels and fsid.levels (I means that I just keep the qdec.table.dat), it works. I can design, display and finally obtain the results. Could anyone give me some suggestions? Any help would be greatly appreciate. Best, Feng

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Automaticky: Jan Sanda is out of the office (příchod 09.11.2015)
by Jan.Sanda＠fnmotol.cz 09 Oct '15

09 Oct '15

Jsem mimo kancelář do 09.11.2015. Poznámka: Toto je automatická odpověď na vaši zprávu "[Freesurfer] PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback" odeslanou dne 10.10.2015 0:58:09. Toto je jediné oznámení, které obdržíte v době nepřítomnosti této osoby.

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PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback
by Frank Scharnowski 09 Oct '15

09 Oct '15

PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback Postdoctoral and PhD positions are available at the University of Zürich, Switzerland. The successful candidate will join a team of real-time fMRI enthusiasts who develop new methods for neurofeedback, and apply them to psychiatric populations (addiction, depression, PTSD). The research agenda involves methods development as well as clinical applications, so anyone with a background in neuroscience, biology, psychology, medicine, computer science, physics, engineering, or related areas is welcome to apply. Previous experience with fMRI is essential. The posts are available immediately, for 3-5 years. Starting salary for postdocs is ~95’000 CHF, and that for PhD students is ~50’000 CHF per year (~6’600/~3’700 CHF net per month, respectively). Zürich offers a thriving international environment, with extensive cultural and outdoor activities and a very high quality of life. Interested applicants should send their CV, a brief statement of research interests, and contact information for 2-3 references. Please feel free to contact me with any questions. Best wishes, Frank -- Prof. Dr. Frank Scharnowski Psychiatric University Hospital Zürich, Switzerland www.neurofeedback-research.org Scharnowski.Frank(a)gmail.com

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mris__label__calc intersect error in longitudinal qcache
by Selvaraj, Bhavani 09 Oct '15

09 Oct '15

Hi, when I try running longitudinal analysis for 2 subjects I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? I saw a similar question in the archived mail list so I tried running this command by itself and this was the comment Segmentation fault I didn't know how to fix this error? should I run them again?? Qdec table Fsid fsid-base years MPS-007_1 MPS-007 3 MPS-007_2mod MPS-007 4 MPS-007_3 MPS-007 4 MPS-005_1 MPS-005 5 MPS-005_2 MPS-005 6 MPS-005_3 MPS-005 6 Thanks, Bhavani

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FAST without preprocessing
by stdp82＠virgilio.it 09 Oct '15

09 Oct '15

Hi list, I'd like to perform FAST preprocessing for functional connectivity (seed-based analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing, motion and slice timing corrections are requested. When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -nostc the analysis is stopped by an error on lacking fmcpr.nii. Thanks Best regards, Stefano

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Freesurfer October 2015