Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Standalone Freeview?
by Jeni Chen 17 Jan '14

17 Jan '14

Hi! I'm wondering if the latest version of Freeview is available in standalone version. I'm currently using FreeSurfer v5.1's tktools for correcting the recon-all outputs, but would like to switch to Freeview. However the version that I have doesn't seem to have the Recon tools, and if I install the latest FS, I will have to rerun the preprocessing... So is it possible to install the latest Freeview separately? Thanks. Jeni Chen

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aseg.stats vs. volumes in native T1 space
by Gabor Perlaki 17 Jan '14

17 Jan '14

Dear all, I've run the freesurfer on 3 subjects and converted the aseg.mgz into *.nii.gz in the native space: "mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii.gz" I've did a stats on left and right hippocampal volumes in the native space using fslstats: "fslstats aseg2raw.nii.gz -l 16.5 -u 17.5 -V" for the left hippocampus and "fslstats aseg2raw.nii.gz -l 52.5 -u 53.5 -V" for the right hippocampus The volumes given by fslstats was about 3% higher than the values reported in the aseg.stats file. The native resolution of the T1 images is 0.45*0.45*0.9 mm^3. I thought that observing a minimal difference could be the consequence of reslicing, but I really don't understand why fslstats gives consequently greater values (for both hippocampi in all three subjects). Thanks, Gabor

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Converting .thickness into nifti volume
by Muhammad Naveed Iqbal Qureshi 16 Jan '14

16 Jan '14

Dear Experts, I need to know how can I convert the .thickness files into volume file that can be opened in SPM and show the thickness of each voxel in the standard templete of the brain. Thank you Best Regards, Muhammad Naveed Iqbal Qureshi

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CUDA problem with FreeSurfer 5.3.0 on CentOS6
by Tran, Kevin (NIH/NIMH) [C] 16 Jan '14

16 Jan '14

Hi, We have encountered a serious problem running recon-all FREESURFER_HOME: /opt/freesurfer-530 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.el6.x86_64 x86_64 The entire command-line executed: /opt/freesurfer-530/bin/recon-all -use-gpu -all -s surface_1 The problem happened when it came to this point mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer-530/average/RB_all_2008-03-26.gca transforms/talairach.m3z nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 6.0 Runtime : 5.50 Acquiring CUDA device Using default device CUDA device: Tesla K20m not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer-530/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.22 (predicted orig area = 6.5) freeing gibbs priors...done. average std[0] = 5.0 AllocateHost: Warning - not thread safe! RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst The same error message kept on repeating and, then, it said ============================================= GPU MRI Label timers -------------------- MarkLabelBorderVoxels Total : -nan ms (avg) 0 ms (tot) VoxInLabelWithPartialVolume Compute : -nan ms (avg) 0 ms (tot) Total : -nan ms (avg) 0 ms (tot) ============================================= CUDA Error in file 'mriconvolve_cuda.cu' on line 945 : unload of CUDA runtime failed. Abort (core dumped) ERROR: mri_ca_register with non-zero status 134 but continuing despite the error We have tried the same data with two different GPUs (Tesla K20m and Quadro K4000). They both had the same problem. Any suggestions? Thanks, -- Kevin Tran, Contractor UNIX System Administrator The National Institutes of Health NIMH, Laboratory of Brain and Cognition 10 Center Drive, Room 4C215 Bethesda MD 20892-1366

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Control point failure - CA Normalize
by Mark Plantz 16 Jan '14

16 Jan '14

Hello freesurfers, I am running into a problem during the "CA Normalize" sequence of autorecon-2. It looks like freesurfer is having a hard time creating control points based off the atlas I am using. The output is as follows: "finding control points in <Left_Cerebral_White_Matter>...found 0 control points" This repeated for the other various regions included in the atlas. The only control points found were "168 control points" in the "Right_Cerebral_White_Matter". Could this possibly be an alignment issue? If so, is there an easy way to check the alignment? Thank you, Mark

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Re: [Freesurfer] mri_glmfit help
by Douglas N Greve 16 Jan '14

16 Jan '14

you have to use your own regressor. This is not usually done with thickness because thickness does not scale with head size On 01/16/2014 04:32 PM, Danielle Miller wrote: > Hi Doug, > > Thank-you for the responses! > > An additional question: does mri_glmfit or preproc take into account > head size? Or will I need to correct for that on my own by including > it as a regressor? > > Thanks, > Danielle > > -- > Ph.D. Program in Behavioral Neuroscience > Boston University School of Medicine L-815 > 72 E. Concord St > Boston, MA 02118 > > > VA Boston Healthcare System Jamaica Plain > Memory Disorders Research Center > 150 South Huntington Ave D11-103 > Boston, MA 02130 > OFFICE:(857) 364-2130 > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_glmfit help
by Danielle Miller 16 Jan '14

16 Jan '14

Hi Freesurfer Experts, I have some questions regarding mri_glmfit - some basic and some not so basic - that I hope you can help me with. 1.) I want to do a thickness analysis looking at the effect of a continuous variable on thickness while regressing out effects of both continuous and categorical variables. Let's just say I have one continuous variable of interest, one to regress out, and one categorical variable (with four groups) to regress out. From reading other posts, it seems that I should make my categorical variables into a class - if I do this will this contrast look at the effect of my continuous variable while regressing out effects from the other variables (including group)? This is assuming I am running a DOSS analysis 0 0 0 0 0 1 2.) In the cluster corrected significant image, I am a bit confused on what the positive and negative significance values represent. If I was looking at group differences - would red indicate that the first group > second group, and blue indicate first group < second group (that is, first group with increased or decreased thickness compared to second group)? 3.) Lastly, I see that you can use mris_preproc and glmfit to look at volume. Does this look at volume in a voxel-based way? That is, is it comparing volume on a voxel level? If so, would the correct commands be: mris_preproc --fsgd FSGD FILE --target fsaverage --hemi lh --meas volume --out OUT.mgh mri_glmfit --y MGH FILE --fsgd FSGD FILE doss --C CONTRAST --surf fsaverage lh --glmdir GLM DIR Would I need to smooth the data? Thanks for any and all help! Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

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data qcached in different FS versions
by Alexander Lebedev 16 Jan '14

16 Jan '14

*Dear Freesurfers,* I have quite a large dataset processed with FS 5.1. However, half of the output was qcached in FS 5.3. I just wanted to clarify whether I should rerun qcache in FS 5.1 for the whole set. If not, could you please confirm that this command does the same across different versions (REF: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19370.html)? Of note, I am going to use unsmoothed output. *===* *Best Regards,* *Alexander Lebedev* Stavanger University Hospital, Norway

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Applying mask with mri_mask
by Arash Jalalian 16 Jan '14

16 Jan '14

Hi, I would like to apply white matter mask (wm.mgz) produced by freesurfer recon-all command on FLAIR. The FLAIR and wm.mgz have different dimensions such that Flair is 512by512 while wm.mgz has 256by256 in dimensions. I tried to fix this by resizing the flair in matlab but after applying the mask the result is not good. I don't get the difference in dimension anymore though. Is there any way that I can resize a mgz volume in freesurfer? Many thanks, Arash

2 1

Folder organization cross-sectional/longitudinal analysis
by Janosch Linkersdörfer 16 Jan '14

16 Jan '14

Hi all, I have 4 years of structural scans from children and 2 from adults. I would like to analyze the data both cross-sectionally and longitudinally. In the recommendations for the longitudinal analysis, it says one should process all images in one folder with the time point in the subjectID/subject folder, e.g., .../data/tp1_subj001 .../data/tp2_subj001 .../data/tp3_subj001 .../data/tp4_subj001 .../data/tp1_subj002 ... For the cross-sectional analyses, I would like to organize the analyses in folders for subject age and year, e.g., .../data/children/tp1/subj001 .../data/children/tp1/subj002 .../data/children/tp2/subj001 .../data/children/tp2/subj002 ... .../data/adults/tp1/adult_subj001 .../data/adults/tp1/adult_subj002 .../data/adults/tp2/adult_subj001 .../data/adults/tp2/adult_subj001 Is it possible to organize the data this way and to symlink the individual folders into another folder for the longitudinal analysis, i.e., .../longitudinal_analysis/tp1_subj001 -> .../data/children/tp1/subj001 .../longitudinal_analysis/tp2_subj001 -> .../data/children/tp2/subj001 ... Additionally, are there any considerations regarding renaming/moving subject folders (as long as anything inside a subject folder remains unchanged), i.e. are there any hard links or similar that would break further processing? Thanks a lot! Janosch

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Freesurfer January 2014