Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

how to add skull and scalp and how to convert RAS coordinates
by Chiara Bulgarelli 19 Apr '16

19 Apr '16

Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues: 1. How can I add the CSF, the skull and the scalp in my model? I know that with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01(a)mail.bbk.ac.uk // bulgarelli.chiara3(a)gmail.com

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Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04
by Nasos Petridis 19 Apr '16

19 Apr '16

Hello, Recently, I started using freesurfer on a Ubuntu system. I've noticed two issues, when using tkmedit, for example: tkmedit subj_name norm.mgz -segmentation aparc.a2009s+aseg.mgz (i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is created, and it can be opened in any image viewing program but is black. It's worth noting that when I try to save a cortical thickness surface view as tiff, using tksurfer tools, it works fine. (ii) When I try to rotate the volume (Tools > Volume > Rotate Volume), I cannot enter an angle in the "Degrees" dialogue box, ie I type the number but no number appears neither doe the cursor move. I've tried both freesurfer 5.3 Linux distributions (centos4, centos6) with no difference. I'm running Ubuntu 14.04LTS. Do I need to install any packages in Ubuntu? Any suggestion how to tackle those two issues would be greatly appreciated. Many thanks, Nasos

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Export Freesurfer labels to SPM ROIs
by Mohamed Abdelhack 19 Apr '16

19 Apr '16

Hello FS community, I have made some custom labels based on retinotopy data and I wish to export these as SPM ROIs so that I can use some specific tools. I grouped the labels into an annotation file and I used mri_label2vol to convert it into nifti, I then imported it into matlab and I get a volume with each pixels corresponding to a number. How can I confirm if the coordinates that I have used to export these labels are aligned well with the data in SPM coordinate system? Thank you, Mohamed,

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How to find the information from MRI data file
by Muhammad Naveed Iqbal Qureshi 18 Apr '16

18 Apr '16

Hi, How can I find the following information from the MRI volume data already preprocessed with Freesurfer. 1. Echo time 2. Repetition time 3. Flip angle Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

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Research Assistant and Psychologist Positions at Max Planck Institute-CBS, Leipzig, Germany
by Katharina von Kriegstein 18 Apr '16

18 Apr '16

Applications are welcomed for two positions in the Human Communication group lead by Katharina von Kriegstein at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany. Research in the group focuses on the investigation of neural mechanisms of human communication using a broad spectrum of neuroscientific methods (functional and structural MRI, MEG, tDCS, TMS). Research involves typically developed populations as well as populations with developmental communication deficits (developmental dyslexia, autism spectrum disorder, phonagnosia, proposagnosia). Research Assistant: http://www.mpg.de/10451891/research-assistant-lab-manager The position will involve recruiting participants, running behavioural tests, assistance with data-acquisition in MRI, TMS and tDCS studies, assistance with data analyses, grant writing and literature searches, attending lab meetings, supervising undergraduate students in the lab and overseeing day-to-day lab operations. The position is available part or full time. It includes the opportunity to pursue a variety of research opportunities that can result in authorship on academic publications. Psychologist: http://www.mpg.de/10451838/20161504-1 (in German) The position is available part time. The main duty will be to support diagnostic testing in people with communication disorders (e.g. autism spectrum disorder, dyslexia, developmental prosopagnosia). The position offers the possibility to be involved in research. For further information on the positions and instructions on how to apply please follow the links provided above. --- Katharina von Kriegstein Max Planck Research Group Leader Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Professor of Cognitive and Clinical Neuroscience Humboldt University of Berlin Rudower Chaussee 18, 12489 Berlin, Germany Phone +49 (0) 341-9940-2476 Fax +49 (0) 341-9940-2448 http://www.cbs.mpg.de/independent-research-groups/human-communication

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Freesurfer 6.0 Hippocampal Subfield Analysis
by Ajay Kurani 16 Apr '16

16 Apr '16

Hello Freesurfer Experts, I am having a bit of trouble with the hippocampal subfield analysis using the Freesurfer 6.0 program. My data is organized as /AnalysisFolder/Group/Subject/Anatomical/SUB_FS .. where SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ and my subject specific folder is SUB_FS. Not all data is located in /Anatomical but rather in /Group for each group. I ran the following based on https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation: recon-all -s ${sub}_FS -openmp 4 -itkthreads 4 -hippocampal-subfields-T1 cd $SUBJECTS_DIR/${sub}_FS/mri/ kvlQuantifyHippocampalSubfieldSegmentations.sh This created 6 files: lh.hippoSfLabels-T1.v10.1mm.mgz lh.hippoSfLabvels-T1.v10.mgz lh.hippoSfVolumes-T1.v10.txt rh.hippoSfLabels-T1.v10.1mm.mgz rh.hippoSfLabvels-T1.v10.mgz rh.hippoSfVolumes-T1.v10.txt I received the following output error in the terminal even though files were generated: kvlQuantifyPosteriorProbabilityImages /usr/local/bin/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:217: itk::ERROR: MGHImageIO(0xe1a620): Can't find/open file: posterior_Left-Hippocampus.mgz /usr/local/bin/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 2000993 Aborted (core dumped) kvlQuantifyPosteriorProbabilityImages /usr/local/bin/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /usr/local/bin/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt When I open lh.hippoSfVolumes I see the following: Hippocampal_tail 403.806174 subiculum 309.796102 CA1 384.206539 hippocampal-fissure 143.951401 presubiculum 226.899518 parasubiculum 49.511870 molecular_layer_HP 381.834418 GC-ML-DG 196.542924 CA3 155.112708 CA4 181.563384 fimbria 31.116787 HATA 26.871413 Whole_hippocampus 2347.261836 I also found a second set of instructions for quantifying Hippocampal subfields: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields This page says to use : quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> so I ran: SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ cd $SUBJECTS_DIR/${sub}_FS/mri/ quantifyHippocampalSubfields.sh T1-${sub}_FS test.txt $SUBJECTS_DIR/${sub}_FS/mri No file was generated for this subject in $SUBJECTS_DIR/${sub}_FS/mri (1)My question for kvlQuandify is if posterior_Left-Hippocampus.mgz is supposed to be created or if this is a file that was generated from a previous version of the program that is supposed to be removed from kvlQuantifyHippocampalSubfieldSegmentations.sh for Freesurfer v6.0 dev? If it is supposed to be created, I do not see this file in /mri for any subjects I tested this script on. (2) Can I use kvlQuantifyHippocampalSubfieldSegmentations or quantifyHippocampalSubfields to calculate each individual subject's volumes for each segment generated in Freeserfer 6.0? Which is the correct program to use? The reason for not using the whole group of subjects with one of these tools is that I want to use SPSS to correlate each subfield volume with at variety of clinical measures, however I may be using these tools incorrectly and there may be a better way to do this. Thanks, Ajay

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Re: [Freesurfer] PET voxelwise
by Elijah Mak 15 Apr '16

15 Apr '16

Dear Doug, One more question: There are many voxels with negative binding potentials in this dataset, mostly in the CSF/ventricular regions. Can I restrict the mri_glmfit to focus only on the voxels with positive BP? Best Wishes, Elijah

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preproc-sess error opening tmp brain_mask
by Mcnorgan, Christopher 15 Apr '16

15 Apr '16

I was hoping the developers might be able to help with a problem I'm having with a sub-step of preproc-sess. I executed the following: preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold In the relevant output, I see mktemplate-sess completed, followed by a call to mkbrainmask-sess, which eventually reported: # ---------- Using FSL's BET to Extract Brain------------------ # /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer/bin/bet.fsl: 231: /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_2623/brain_mask.nii --min .01 --o /tmp/mkbrainmask_2623/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_2623/brain_mask $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold cmdline mri_binarize --i /tmp/mkbrainmask_3238/brain_mask.nii --min .01 --o /tmp/mkbrainmask_3238/brain_mask.nii sysname Linux hostname wernickesarea machine x86_64 user chris input /tmp/mkbrainmask_3238/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_3238/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 It's not obvious from the tail end of the output that this didn't work out, but this process finished in just a couple of seconds (making it unlikely that any smoothing or slice time correction was performed), and there was no brain_mask.nii file to be found either in /tmp/ or in the session folder. Those "not found" errors seem relevant, but I can't imagine what to do about them.

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mri_vol2surf after recon-all
by Trisanna Sprung-Much 15 Apr '16

15 Apr '16

Hi Freesurfer I have some labels (.mnc) that are painted voxels generated from a Montreal Neurological Institute software. I am trying to project the labels onto the surfaces generated from recon-all that I applied to the corresponding MRI volumes. *I used mri_vol2surf: * mri_vol2surf --src labels.mnc --out test.mgz --srcreg talairach.auto.xfm --hemi lh *and got the following error:* Error reading inplaneres from talairach.auto.xfm Do I need a .dat file? If so, how can I attain it? Essentially, what is the registration file that I am supposed to be using? Many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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correcting mri_glmfit results
by Clara Kühn 15 Apr '16

15 Apr '16

Dear FreeSurfer experts, I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm with this: mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh --cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir So far so good :) Now when I try to apply the Monte Carlo correction with this: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 --2spaces I get the error "fwhm: Undefined variable." So I tried to run the glmfit with the --y flag and use the lh.thickness_sm10.mgh file but I created that when registering and smoothing ALL my time points to the template, so I get this error: "ERROR: dimension mismatch between y and X. y has 224 inputs, X has 72 rows." I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm only an overwriting one. Should I register and smooth the data again for the separate time points or is there another way to deal with that? What could I do to correct my glm data? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Freesurfer April 2016