Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

samseg permissions error
by Russo, Andrew William 06 Mar '20

06 Mar '20

Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew ____________ Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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Re: [Freesurfer] Apply transformation
by Adam Rytina 06 Mar '20

06 Mar '20

External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam ________________________________ Od: Adam Rytina <adam.rytina(a)outlook.cz> Odesláno: středa 19. února 2020 8:11 Komu: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Předmět: Fw: [Freesurfer] Apply transformation Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> za uživatele Adam Rytina <adam.rytina(a)outlook.cz> Odesláno: sobota 15. února 2020 19:52 Komu: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Předmět: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> za uživatele Douglas Greve <dgreve(a)mgh.harvard.edu> Odesláno: sobota 15. února 2020 17:15 Komu: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Extract specific LGI and Volume values
by Tien Pham 06 Mar '20

06 Mar '20

External Email - Use Caution Dear FreeSurfer Experts, I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my longitudinal results using QDEC to draw the ROIs which is showed significant differences, label it and map to all subjects. Then I get the LGI value of the ROI I saved before using the command below: cd $SUBJECTS_DIR mris_anatomical_stats -l lh.untitled.label \ -t lh.pial_lgi \ -b \ -f subject_id/stats/lh.untitled.stats subject_id lh And this is the result: [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mris_anatomical_stats -l lh.frontoinsula.label \ ? -t lh.pial_lgi \ ? -b \ ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh limiting computations to label lh.frontoinsula.label. using thickness file lh.pial_lgi. reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz... reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... reading input pial surface /applications/freesurfer/subjects/VC019_1/surf/lh.pial... reading input white surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 6595 4368 15935 3.311 0.895 0.158 0.077 135 19.7 lh.frontoinsula.label As I saw there was no columns showing the LGI value, I did similar with gray matter volume, the result displayed the different in some values of the columns. Could you please help me to explain about this? Thank you very much. Best regards, Tien Pham

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Issue with BBR and Applying CVS Warps to Diffusion Data
by Austin Patrick 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison

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registrations
by Octavian Lie 06 Mar '20

06 Mar '20

External Email - Use Caution Dear All, I need to register: 1. T1.mgz to a T1 postresection volume (no contrast), with large resection. Which one should I use, mri_robust_register, or bbregister, if the latter, which is the better initiator (nmi, spm, fsl)? 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space recon-all flag), which FS registration tool should I use? 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask. I would appreciate commands (either names, or full command lines), please advise. Thank you, Octavian

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group analysis for same group in 2 conditions
by Marco Ninghetto 06 Mar '20

06 Mar '20

External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which each participant undergoes to 2 different conditions. One in normal sight (NG, i.e.: No Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes Goggles). I'd like to compare the results between these two conditions (basically, subject A, B, C in cond1 versus subject A, B, C in cond2). I created the FSGD file (attached as "RetinotopyStudy" file) and the contrast matrices, organised as: 1 -1 , named "YG-NG.mtx" > -1 1, named "NG-YG.mtx" In this FSGD sample file, I reported only subjects from 7 to 12. My folders are organised as follows: main >> recon_output >> sub-yy (X folders for X subjects) > >> Contrasts (with contrast files) > >> FSGD (with FSGD files) > >> fsaverage (subjects template > created during recon-all -qcache) > >> pRF_function >> analNG (inside, there are the functionals for > each subject in NG condition) > >> analYG (inside, there are the > functionals for each subject in YG condition) Once I used the pipeline for the retinotopy analysis <http://freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysis>and I have results for each participant, and now I'd like to make 2nd lev analysis. So the idea would be, as you probably already got it, condition Yes Goggles versus condition No Goggles. I use the command: mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out > outputname.mgh But I'm not sure it would calculate in the right way. The question is: how would I organise the FSGD file or folders in such a way that FREESURFER would know that it has to compare results from the same subjects but from two different folders (analNG vs analYG)? Hoping that's clear, I really look forward to hear from you soon. Thank you for your time, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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some basic questions regarding longitudinal analyses in Freesurfer
by Lara Foland-Ross 06 Mar '20

06 Mar '20

External Email - Use Caution Hello, I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the intra-subject registration failed in the longitudinal processing stream. For this reason, my data were not initially processed using the longitudinal processing stream within Freesurfer. However, per this thread - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html - I still plan to use the LME model. As I understand it, this model assumes that the longitudinal processing stream was conducted. Therefore, I have the following questions: 1. would the "base" (aka within-subject template) for each subject be = time point 1? 2. would the "long run" for each subject be = each subject's individual time points? 3. assuming #1 and 2 are correct, would I need to set my directory structure to match that used in the longitudinal processing stream? For example, if I have 2 time points for subject 1234, and they are initially labeled "1234.time1" and "1234.time2", then in order to run the LME model, I would create a copy of "1234.time1" and rename the copy as "1234" to indicate to the software that this should be used as the base. And, I would also need to rename "1234.time1" and "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to indicate that these folders should be used as the longitudinal time points. Does this seem appropriate? Thanks in advance for your help, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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mri_vol2surf produces invalid surface
by Shuntaro Aoki 05 Mar '20

05 Mar '20

External Email - Use Caution Dear mailing list, I was trying to convert a volume image to a freesurfer surface (as gii) with `mri_vol2surf` for visualization, but ended up with invalid surface data (i.e., a file not loadable by freeview). What I did was: --- % mri_vol2surf --version stable5 % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub --hemi lh --out ./sample_vol2surf_lh.gii --- Here, `sample_volume.nii.gz` is a volume image (such as a statistical map) registered to an individual reference T1w image of subject `sample-sub`, which was the input of recon-all for the subject. The command completed without errors: --- srcvol = ./sample_volume.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz as target reference. Reading surface /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 31055 Writing to ./sample_vol2surf_lh.gii Dim: 155685 1 1 --- Then I tried to open the resulting surface `sample_vol2surf_lh.gii` with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed to load Surface". I also got the following shell output: --- mriseadGIFTIfile: mris is NULL! found when parsing file /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii MRISread failed mriseadGIFTIfile: mris is NULL! found when parsing file /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii --- The output of `mris_info` is: --- % mris_info sample_vol2surf_lh.gii ================================================== gifti_image struct version = 1.0 numDA = 1 gim->meta nvpairs struct, len = 3 : nvpair: 'UserName' = 'aoki' nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020' nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 2010' gim->labeltable giiLabelTable struct, len = 0 : -------------------------------------------------- gim->darray[0] giiDataArray struct intent 0 = NIFTI_INTENT_NONE datatype 16 = NIFTI_TYPE_FLOAT32 ind_ord 1 = RowMajorOrder num_dim = 1 dims = 155685, 0, 0, 0, 0, 0 encoding 3 = GZipBase64Binary endian 2 = LittleEndian ext_fname = ext_offset = 0 darray->meta nvpairs struct, len = 0 : data = <set> nvals = 155685 nbyper = 4 numCS = 0 darray->ex_atrs nvpairs struct, len = 0 : -------------------------------------------------- gifti_image struct swapped = 0 compressed = 1 -- darray totals: 1 MB gim->ex_atrs nvpairs struct, len = 0 : ================================================== --- I checked matching between voxels in the input volume and the surface with the output of --srchit option and found the registration was fine. I also tried mgh output but got another invalid file. --- % mris_info sample_vol2surf_lh.mgh ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! No such file or directory --- I would appreciate any advice on this. Regards, Shuntaro -- ---------------------------------------- Shuntaro C. Aoki, Ph.D. Program-specific Researcher Neuroinformatics group Graduate School of Informatics Kyoto University s_aoki(a)i.kyoto-u.ac.jp ----------------------------------------

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timeseries question
by Nasiriavanaki, Zahra 02 Mar '20

02 Mar '20

Hi Freesurferes I have extracted timeseries from a task fMRI using the command below: mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh rh.label --id 1 --avgwf-remove-mean --avgwf ./rh.txt My question is: Is the temporal drift being counted in considering that I used preprocessed data as the input? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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make_average_subject
by Benjamin Ineichen 02 Mar '20

02 Mar '20

External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 I get an error message - ERROR: make_average_surface. Please find attached the error.log. Would be very thankful for advice! Many thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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Freesurfer February 2020