Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Re: [Freesurfer] pwd: permission denied
by Marcel Zwiers 07 Mar '12

07 Mar '12

Hi Michael, Thanks for your help and suggestions! > I'd have to try to recreate the error, but I have an idea of what it > could be (assuming > /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness/BIG1026_1 > is a directory). Actually not yet, /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness is a directory but BIG1026_1 is supposed to be created by recon-all (but wasn't as a consequence of the error). > While you may have read, write, and execute permissions to your > colleague's directory, you must make sure that these permissions have > been recursively added to the contents of that directory (child > directories, child directory files, and directory files). There are only *.nii.gz files in that directory plus a few extra files and (symbolic links to) folders that I assume should have nothing to do with the error? The content looks like this (ls -al): drwxrwxr-x 2 marhoo big 352256 Mar 6 09:51 ./ drwxrwx--x 15 marhoo big 4096 Feb 29 15:49 ../ -rw------- 1 marzwi big 12219623 Mar 2 16:06 BIG1026_1.nii.gz [..] -rw------- 1 marzwi big 12219623 Mar 2 16:06 BIG4025_1.nii.gz -rw-rwxr-- 1 marhoo big 75806 Feb 27 10:54 BIG_aseg_stats.log* lrwxrwxrwx 1 marhoo big 34 Feb 19 09:12 fsaverage -> /opt/freesurfer/subjects/fsaverage/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 lh.EC_average -> /opt/freesurfer/subjects/lh.EC_average/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 rh.EC_average -> /opt/freesurfer/subjects/rh.EC_average/ -rw-rwxr-- 1 marhoo big 18200 Sep 27 10:39 v5.0.txt* -rw-rwxr-- 1 marhoo big 3220 Sep 27 10:39 v5.1.txt* -rw-rwxrw- 1 marhoo big 523 Feb 24 10:07 .xdebug_tkmedit* > I believe that your problem is that the file BIG1026_1.nii.gz > (however, from my experience this file should not simply be in the > BIG1026_1 folder but in the orig directory of the mri folder) has not > inherited the specified permissions from its parent directory. My username is marzwi, I am member of the big group and I have rw permissions of all the files and directories (see listing above) . > If this does not correct the error, set the environmental SUBJECTS_DIR > variable to the directory housing the subject directories (making sure > that your colleague gives you sufficient access to this directory), > lose the -sd path in the command, and make sure that you have read, > write, execute permissions recursively added to the directories and > files that you will be working with. I did that but the error message remains. Here's the full message, started from a newly opened bash terminal: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer FSFAST_HOME /opt/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer/subjects MNI_DIR /opt/freesurfer/mni FSL_DIR /opt/fsl mentat002:$ export SUBJECTS_DIR=/home/mrphys/marzwi/BIG/Freesurfer_CorticalThickness mentat002:$ recon-all -subject BIG1026_1 -i BIG1026_1.nii.gz -autorecon1 /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied cp: cannot create regular file `/BIG1026_1/scripts/build-stamp.txt': No such file or directory cat: /BIG1026_1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is Actual FREESURFER_HOME /opt/freesurfer-v5.1 /BIG1026_1: No such file or directory. > Another option would be if your colleague set up a "subjects > directory" within his parent directory and add each subject's folder > to this directory and then setting this as your SUBJECTS_DIR variable > (ensuring you have read, write, execute permissions). I created a subfolder, copied the BIG1026_1.nii.gz file into it and ran recon-all using this subfolder as SUBJECTS_DIR but I kept getting permission denied errors. > I hope this helps; however, not knowing the version of free surfer > that you are running nor the operating system makes it difficult to > trou bleshoot your problem. Let me know if you arrive at a solution or > require further assistance. > Thanks, > Michael Nowak I hope the info above can help troubleshooting my problem. Thanks a lot Michael! Cheers, Marcel On Mon, Mar 5, 2012 at 9:55 PM, Marcel Zwiers < m.zwiers(a)fcdonders.ru.nl > wrote: > Hi, > > I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier > postings on. When I run recon-all on a file in my own home directory everything works normally: > > recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz > -autorecon1 > [..] > > However, if I run the same command on the same file, except that this file is now located in a directory of a > colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: > recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects > /BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 > pwd: cannot open directory `../..': Permission denied > /bin/pwd: cannot open directory `../..': Permission denied > mkdir: cannot create directory `/BIG1026_1': Permission denied > [..] > > From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have > full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause > and hope you have any ideas here. > > Cheers, > Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands

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qdec
by Richter, Julia 07 Mar '12

07 Mar '12

Dear Sir or Madam, I have a question concerning FreeSurfer. At the moment I am trying to run a qdec analysis. I have already written the qdec.table.dat (attached, labeled test.dat) and a file labeled diagnosis.level.dat, in which all possible levels are listed (also attached). When I try to load the data table, I get an error message (as you can see in the attached screenshot). Can you please help me to solve the problem? Thanks a lot, yours sincerely, Julia Richter

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How to find the anatomical slices in the data?
by bowang21＠mail.ustc.edu.cn 07 Mar '12

07 Mar '12

Dear All, Now I have some datas which are including anatomical data and function data,and I want to find the anatomical slices from them to run command 'recon-all'.How can I do? Yours

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About new FS version
by Gabriel Gonzalez Escamilla 07 Mar '12

07 Mar '12

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poor image quality and re-running freesurfer
by Christine Smith 06 Mar '12

06 Mar '12

Hello, I have a couple of subjects with poor quality scans. The grey/white contrast is not so good. I wonder if the newest version of freesurfer might help with the pial and white surfaces. Do I need to make some minor edits to key images/files in order to force freesurfer to take a second shot at these subjects? For example, can I just rerun these subjects with the new version? Or do I need to make some edits in order to have freesurfer re-evaluate the brain mask, wm.mgz, and surfaces. For example, should I make a minor edit to the brainmask.mgz and the wm.mgz files in order for freesurfer to detect that it needs to redo those parts. Thank you, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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About recon-all
by bowang21＠mail.ustc.edu.cn 06 Mar '12

06 Mar '12

Dear all, I have just ran the command 'recon-all'. recon-all -i 3098704 -s BianYP -sd /home/wb/test/ -all In the parameters,3098704 is a function slice,but this parameter need a anatomical volume.Could it can find the correct ones itself? Whether the anatomical volume is just 3D slice or 2D ?

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Flags to align per-run motion-corrected functional volumes?
by Alex Kell 06 Mar '12

06 Mar '12

Hi Freesurfers, I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion correction (these subjects have a lot of between-run motion), and I want to analyze the volumes in each subject's individual space (I'd prefer native functional space, but I am happy to do it in each subject's anatomical space). Do preproc-sess, mkanalysis-sess, or selxavg3-sess have any built-in flags that would automatically align the functional volumes using the 6 rigid parameters generated from bbregister? Or do they have a built-in way to align and to upsample the functional volumes to the subject's anatomical space (not the surface)? I am happy to upsample each run's functional volume to anatomical space with an mri_vol2vol call, and then to estimate my glm with selxavg3-sess on these volumes. But I figure there may be some flags that do this automatically. I've looked through the documentation and I haven't found these flags. Is this possible to do automatically? Thanks, guys! Alex Kanwisher Lab Manager McGovern Institute for Brain Research MIT

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Experiences with GPU-assisted recon-all
by Abdulkadir Ahmed 06 Mar '12

06 Mar '12

Dear SPM community, Freesurfer supports GPU acceleration since version 5.0. To assess the utility of this functionality, particularly the gain in performance, I performed `recon-all` with and without the option `-use-gpu`. I'd like to share the result and also hope to get some answers to the question that came up. The Video card used was a GeForce GTX 460 and the CPU was an Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz. 1) cudadetect did not recognize the video card Detecting CUDA... *** No CUDA enabled device(s) detected! *** 2) mri_em_register_cuda called without parameters gave following output nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 3.20 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: GeForce GTX 460 ... 3) Running mri_em_register_cuda was about 4 times faster than mri_em_register. During execution of mri_em_register_cuda, the GPU load was at 20% as indicated by `nvidia-smi -a` 4) Running `recon-all` with `-use-gpu` option took 6:49 hours and without the option it took about 20 Minutes longer. A summary of the processing steps taken from `recon-all-status.log` is attached to this email. Note, that these times represent wall clock times, not CPU times. Hopefully this information will be helpful. The processes "EM Registration" and "CA Normalize" were significantly accelerated by the GPU, as expected. Also "SubCort Seg" ran much faster. "Surf Reg rh" ran 3.4 times faster with GPU acceleration while the accelerated version of "Surf Reg lh" was slower than the regular. What binary was used in these steps? What could be the reason for the difference between hemispheres (I assume lh/rh means left/right hemisphere)? Bug? Problem with the data? According to `-recon-all`, following binaries support GPU acceleration mri_em_register, mri_ca_register, mris_inflate and mris_sphere. Cold someone point out what binaries correspond to the 64 steps reported in the "scripts/recon-all-status.log"? This would enable to identify the steps that have GPU-accelerated variants. The GPU performance was at 20% while CUDA binaries were executed. What could be the reason for this, i.e. why not 100%? Is this even expected on the GeForce GTX 460? What are the limitations when running multiple GPU-accelerated instances of `recon-all`? How many GPU memory does a single instance take at max? What could be the reasons that `cudadetect` failed to detect any CUDA devices, yet CUDA binaries worked as expected? Best regards, Ahmed Abdulkadir -- Master Student, Life Sciences, Semester 4 Medical Image Processing (MIP) Lab École Polytechnique Fédérale de Lausanne Student Assistant Functional Brain Imaging (FBI) Department of Neurology University Medical Center Freiburg Breisacher Str. 64, D-79106 Freiburg --

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Re: [Freesurfer] Output volume defined by pial surface/red line
by Douglas N Greve 06 Mar '12

06 Mar '12

Yes, you can do this in a few steps. Use mri_binarize to convert the ribbon.mgz into a binary mask of just the cortex (use the --match option). Then use mri_binarize with aseg.mgz to get the hippocampus (17 for left, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then add them together with fscalc. Then use mri_mask with brain.mgz as the input and the result from above as the mask. doug octavian lie wrote: > Dear Bruce and Doug, > > I want to clarify what I need. > I would need to export to nii.gz a brain volume which has to be : > - T1, > - contain gray and white matter inside the pial surface, without > white-gray segmentation (the source analysis program downstream in the > pipeline needs to complete this step in order to function). > - in addition to the pial contents, it should contain > hippocampi/amygdala as per aseg process, but exclude cerebellum > - the volume inside the pial surface has to be "real", not binary.(if > binary, gray should be darker than white, and not sure if this would > work with the source analysis program I run). > > If I try to export volumes such as brain.mgz, or brain.finalsurf.mgz, > the extra dura/scalp *outside* of the pial surface (red line, fig) is > also exported. Again, I am working at editing the pial surface to > remove extra dura inside the red line; this is a work in progress, > including customizing early recon-all steps/ implenting Andre's > protocols. My problem is how to exclude tissues* outside* the pial > surface/ red line, except hippocampi/amygdala. > Can I create a pial/hippocampal mask excluding everything outside the > red line/hippocampal/amygdalar volumes, which then I could align to a > "real" brain, such as brain.mgz to get the brain inside the calculate > pial surface? If so, how you would proceed? > > Thank you for your suggestions. > > See also my previous message: > > > Dear All, > > I am increasingly fascinated by freesurfer. > Here is a rookie issue: I use a source imaging program that is rather > simple-minded in its MRI processing steps. To be able to use the > inverse solution tools of that program, I need to use 2 volumes: > - a head MRI to be used to electrode coregistration > - a skull-stripped brain MR without cerebellum, including both the > gray and white matter; the program needs to perform its own white > matter extraction to generate the gray matter volume to be used as > source space. > - both MRs have to be subject to the same transforms, if any, and have > to have the same origin and coordinate systems (like real > head/brain pairs). > > So first, I am in the search of the "best" brain extraction possible, > with as little dura included as possible. Besides trying to > implement Andre's dura protocols, and editing the pial surface for > brainmask.mgz, then running the rest of the recon-all steps, I need > to be able to export in nii.gz format a volume having its pial surface > as calculated by freesurfer. > When exporting brain.finalsurfs.mgz with mri_convert, it looks that > the calculated pial surface (red line) as visualized with tkmedit subjid > brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the > output nii volume is imported in programs such as Bioimage Suite, > I essentially see what looks like the outside (surface) brainmask.mgz > volume as in tekmedit but not accounting for the calculated pial > surface. How can I export brain.finalsurfs.mgz with its calculated > pial surface as a nii volume? In other words, I would need a > ribbon.mgz type volume to include the white matter on the inside. I > suppose it comes down to adding options to the mri_convert > brain.finalsurfs.mgz step after surfaces have been generated, but I > would need some guidance > Please advise. > > > Octavian. > > > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Matched sample
by Jacquelynn Nicosia Copeland 06 Mar '12

06 Mar '12

Hi there FreeSurfers, I was thinking about using a propensity matched control sample for a study I am conducting that includes FS data. I would want to match each patient (i.e., MCI) with a specific control (re-using some controls multiple time(s) using the propensity matching, and then using paired sample statistics. However, when looking on FS about qdec and group analyses using the command stream, I didn't see any information about if/how to set up a paired sample. Is it possible to do a matched paired sample (reusing control pts) with FS? If so, where I could get more information on it? Thank you, Jacquie Jacquelynn N. Copeland, M.A. Doctoral Candidate Medical/Clinical Psychology Program Department of Psychology University of Alabama at Birmingham Email:jcopeland@uab.edu ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Tuesday, March 06, 2012 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 97, Issue 8 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. controls points in 5.1 (Chris Hyatt) 2. mri_vol2surf error writing to nifti volume (Tina Jeon) 3. mri_cvs_register on a 64-bit Mac crash PETSC ERROR (Rey Ramirez) 4. (no subject) (Ryan) 5. overlaying sig.mgh onto normalized individual brains (Catherine Wan) 6. Re: (no subject) (Bruce Fischl) 7. Ask question about QAtools (chenchunhuichina) 8. Re: pwd: permission denied (Marcel Zwiers) 9. Re: mri_cvs_register on a 64-bit Mac crash PETSC ERROR (Bruce Fischl) 10. about QAtools (chenchunhuichina) 11. About recon-all (bowang21(a)mail.ustc.edu.cn) 12. Re: About recon-all (Bruce Fischl) 13. Research scientist in MRI imaging ? three-year contract available immediately (Fr?d?ric Andersson) 14. Re: about QAtools (Louis Nicholas Vinke) 15. PhD / Post-Doctoral position ? Neuroimaging of language and audition, University of Geneva (Narly GOLESTANI) ---------------------------------------------------------------------- Message: 1 Date: Mon, 05 Mar 2012 16:48:24 -0500 From: "Chris Hyatt" <Chyatt(a)harthosp.org> Subject: [Freesurfer] controls points in 5.1 To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4F54EE580200002D0002B061(a)gwmail1.harthosp.org> Content-Type: text/plain; charset=US-ASCII Bruce, You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag. I too had noticed very different behavior after adding control points in v5.0 and v5.1, as many more regions were tagged as white matter in v5.1 than in v5.0. Would anyone know if this flag exists and how to use it? Thanks, Chris Re: [Freesurfer] control point guidanceBruce Fischl Fri, 27 Jan 2012 11:58:38 -0800 Hi Mikeit's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect.Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know.Bruce ------------------------------ Message: 2 Date: Mon, 5 Mar 2012 21:55:38 +0000 From: Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> Subject: [Freesurfer] mri_vol2surf error writing to nifti volume To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <C567682DBD3D104CA75A281451264BA301E4B5FC(a)swmsmailstu.swmed.org> Content-Type: text/plain; charset="us-ascii" Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Freesurfer March 2012