Freesurfer

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30064 discussions

FIR analysis
by Sarah Cole 15 Feb '18

15 Feb '18

Hi experts, I was wondering if there is any tutorial or example on FIR analysis. I don't know where to start. I need to look at the time course of some voxels. I have a localizer session and the main experiment. I am intending to find the ROIs in the localizer scans and then extract their time course activation in the main experiment scans. I have done the recon-all successfully. Then in my localizer scan, I did preproc-sess, mkanalysis-sess with FIR 6 24 flag, mkcontarst, and selxabg3. Now, I am lost. Sorry for my naiive question. Thank you, --SC

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inter-hemisphere registration on customised template
by Ting Qi 15 Feb '18

15 Feb '18

Dear Freesurfer experts, I am writing to ask how to do the surface-based inter-hemispheric registration based on the customised template, instead of fsaverage. I am planning to calculate the lateralisation index for each vertex, which means I should to use the symmetry template, for example, fsaverage_sym. However, the current issue is my participants are children. Therefore it would be better to put the individual data to the customised average template, which is already created by ANTS in my case. So I was wondering how to perform the symmetry registration on this created template? Thank you in advance. Cheers, Ting

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Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM
by Simon, Joe 15 Feb '18

15 Feb '18

Dear Experts I just recently started using Freesurfer (implemented as a virtual machine on a Windows machine). After having completed the recon-all procedure, I now want to export the subcortical segementation as .nii images for further use in SPM. My aim is to have a ROI for each segmented subcortical structure. What would be the easiest way to do this? Any help is appreciated. Thanks a lot! Best regards, Joe ---------------------------------------------------------------- Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik Im Neuenheimer Feld 410 69120 Tel.: ++49(0)6221-56-38667 joe.simon(a)med.uni-heidelberg.de ----------------------------------------------------------------

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Re: [Freesurfer] Longitudinal TRACULA study
by Yendiki, Anastasia 14 Feb '18

14 Feb '18

Hi Donatas – All sounds fine. You can process single time points, and you can process subsets of time points if the DWI data from one of them is unusable. The T1 base template is only used as a reference space for longitudinal TRACULA, so it shouldn’t make a huge difference if one additional time point was used to generate that T1 base template (assuming of course that there wasn’t a huge morphological difference in that specific time point that would make the base template much different if it had been generated without that time point). Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Donatas Sederevicius <donatas.sederevicius(a)psykologi.uio.no<mailto:donatas.sederevicius@psykologi.uio.no>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, January 31, 2018 at 4:51 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Longitudinal TRACULA study Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processed structural data using FS longitudinal pipeline and got the following: base_101 sub101_01.long.base_101 sub101_02.long.base_101 sub101_03.long.base_101 Now I want to run longitudinal TRACULA processing. If all data is OK after quality checking (struct and DWI) I could set the configuration file as follows: set subjlist = ( sub101_01 \ sub101_02 \ sub101_03 ) set baselist = ( base_101 \ base_101 \ base_101 ) It turns out that DWI data of sub101_01 is extremely distorted and cannot be used for processing. Should I re-process struct data based on the last two timepoints or is it perfectly fine to use the base and long derived from all timepoints although I’m running tracula for the last two timepoints of DWI? In addition to that, is it fine to run longitudinal TRACULA on a list of subjects where some of them have only one timepoint of data and structural processing underwent longitudinal pipeline for that one timepoint? Thank you for your answers. Best, Donatas

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Status?
by John Davis 14 Feb '18

14 Feb '18

Hi. I'm completely stuck without more input from freesurfer experts. The email was about tracula. Could you confirm that you received my question and that I sent everything you requested? Thanks much. -- John Davis, PhD Cell: (520) 907-9769 jdavis(a)mrn.org

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Masking cortical thickness
by James Hobart 13 Feb '18

13 Feb '18

Hi all, I am looking to mask out a small region of the GM when calculating the cortical thickness of ROIs across the brain. Essentially I have a couple of cases with small GM lesions where the cortical thickness is less likely to be meaningful for my analysis. I have binary lesion masks and also full recon-all s for these cases. I was thinking I would need to mask the cortical thickness map somehow (potentially mapping the mask volume to a surface?) before using the mris_anatomical_stats to calculate cortical thickness. Is this the best way to go about this? Many thanks James

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Re: [Freesurfer] map values to vertices {Disarmed}
by Frederick Barrett 13 Feb '18

13 Feb '18

Thank you, Bruce. I did reconstruct the surfaces from that subject. These are the steps that I've taken: recon-all -s <subid> -i <mprage> -all mris_register <subid>/surf/<hemi>.sphere fsaverag5/<hemi>.?reg.template.tif <subid>/surf/<hemi>.fsaverage5.sphere.reg mri_surf2surf -s <subid> -h <hemi> --sval-xyz <hemi>.pial --trgsubject fsaverage5 --tval <hemi> mri_surf2surf -s <subid --hemi <hemi> --sval-xyz <hemi>.pial --trgsubject fsaverage5 --tval <hemi>.pial.<subid> --tval-xyz <subid>/mri/orig.mgz mris_convert fsaverage5/surf/<hemi>.pial.<subid> fsaverage5/surf/<hemi>.pial.<subid>.asc this final file (fsaverage5/surf/<hemi>.pial.<subid>.asc) was read into MATLAB and MATLAB code generates a continuous value for each vertex (n=10242) for a given subject. I want to map these values back to the surface, but it sounds like if you're recommending mri_vol2surf, that you are saying I should represent these continuous values in a voxel in 3D space, is that correct? Is there an easy way to map the values for each vertex without having to go through a 3D representation? Best, Fred Hi Fred we usually use mri_vol2surf for this kind of thing. Did you reconstruct surfaces from that subject? cheers Bruce On Tue, 13 Feb 2018, Frederick Barrett wrote: Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuous variable (non-integer) to each vertex on a surface so that I can visualize these values on the surface (or an inflated brain), but I can't figure out how to do this. I've projected the pial surface of fsaverage5 to native space within a volunteer, then exported the xyz coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc file using mris_convert. These xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD scan in native space for the subject were read into MATLAB, and I've used a separate toolbox in Matlab to generate weights from the BOLD data that map to each vertex (a continuous variable, one weight per vertex per subject), and these weights can be written to a text file in the following format for each hemisphere: x1 y1 z1 weight1 x2 y2 z2 weight2 ... x10242 y10242 z10242 weight10242 or vertex1 weight1 vertex2 weight2 ... vertex10242 weight10242 or another format if that would be helpful. How can I map these weights back to a surface and visualize it? Please advise. I began to think this fell into the realm of annotation, but it seems that annotations are categorial rather than continuous. Thank you so much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarr...(a)jhmi.edu | frederick.barr...(a)gmail.com NCBI: https://goo.gl/mUKEZm Google Scholar: MailScanner has detected a possible fraud attempt from "scholar.google.com" claiming to be http://goo.gl/vjrrsl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.

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map values to vertices {Disarmed}
by Frederick Barrett 13 Feb '18

13 Feb '18

Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuous variable (non-integer) to each vertex on a surface so that I can visualize these values on the surface (or an inflated brain), but I can't figure out how to do this. I've projected the pial surface of fsaverage5 to native space within a volunteer, then exported the xyz coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc file using mris_convert. These xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD scan in native space for the subject were read into MATLAB, and I've used a separate toolbox in Matlab to generate weights from the BOLD data that map to each vertex (a continuous variable, one weight per vertex per subject), and these weights can be written to a text file in the following format for each hemisphere: x1 y1 z1 weight1 x2 y2 z2 weight2 ... x10242 y10242 z10242 weight10242 or vertex1 weight1 vertex2 weight2 ... vertex10242 weight10242 or another format if that would be helpful. How can I map these weights back to a surface and visualize it? Please advise. I began to think this fell into the realm of annotation, but it seems that annotations are categorial rather than continuous. Thank you so much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarret2(a)jhmi.edu<mailto:fbarret2@jhmi.edu> | frederick.barrett(a)gmail.com<mailto:frederick.barrett@gmail.com> NCBI: https://goo.gl/mUKEZm Google Scholar: http://goo.gl/vjrrsl<http://scholar.google.com/citations?user=KCtXPmAAAAAJ>

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Problems running LGI
by Dusan Hirjak 13 Feb '18

13 Feb '18

Dear Freesurfer Experts, I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS Sierra and I already set up the freesurfer PATH in Matlab. However, I am getting the following error after starting recon all -s localGI : Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s SP002 -localGI Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/NSS_Analysis_01 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 dusan wheel 508655 Jul 29 2017 /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/scripts/recon-all.log Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf #-------------------------------------------- #@# Local Gyrification Index lh Sat Feb 10 21:59:13 CET 2018 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 Any help would be greatly appreciated! Many thanks, Dusan

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quantifyHAsubregions.sh , HBT/FS60/CA
by Eva Hilland 13 Feb '18

13 Feb '18

Hi Eugenio, Is it possible to use *quantifyHAsubregions.sh* to write out the three different hippocampal subfield outputs ? - HBT: the hippocampus is subdivided into head, body and tail. - FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e., no head/body subdivision for the hippocampal subregions. - CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields: GC-ML-DG is absorbed by CA4, and the voxels in the molecular layer are assigned the label of the closest voxel that is neither molecular layer nor background Best Eva

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