Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

FreeSurfer 6.0.0 CentOS 7 compatibility
by Vanzo, Davide 25 Sep '18

25 Sep '18

Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 should be compatible with CentOS 7. However in the official documentation I cannot find any related statement. Moveover, the download web page still shows only CentOS 6 as supported platform. Could you please clarify if the current stable release works correctly on CentOS 7 or not? Thank you. Best regards -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu

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ROI extraction using functional masks
by Yann Quidé 06 Jun '18

06 Jun '18

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, the “end product” does not really look good, some of the extracted ROI for some subjects are empty. Does anyone have a clue of why? Here is what I have done: 1) transform .nii file to .mgz file $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz 2) to make sure our masks from SPM will match fsaverage templates, I did tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5 tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5 It was fine. 3) I created a .dat file containing the registration matrix from avg152T1 onto fsaverage cd $SUBJECTS_DIR/fsaverage/surf spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg $REG_DIR/avg152T1_to_fsaverage.dat 4) Visualisation of the registration tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $REG_DIR/avg152T1_to_fsaverage.dat --surf orig The registration was bad, so… I manually relocate the TAL template onto the fsaverage template and saved a new avg152T1_to_fsaverage.dat file called avg152T1_to_fsaverage_edited.dat. This file is used for the next steps. 5) Visualisation of the registration of our mask onto fsaverage T1 cd $SUBJECTS_DIR/fsaverage/surf tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/L_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/R_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white Up to this sep, everything looks good. 6) Transformation of the ROI mask to surface and thickness mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l $MASKS_DIR/L_ROI.label mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l $MASKS_DIR/R_ROI.label 7) Extraction of the ROI surface and thickness for analyses mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f $OUT_DIR/results_L_ROI_SubjID SubjID lh mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f $OUT_DIR/results_R_ROI_SubjID SubjID rh Thanks to anyone who will be able to help me with that! Yann

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Neuroimaging postdoc position available at the University of Michigan
by Martijn Muller 15 May '18

15 May '18

*Research Fellow - Multimodal neuroimaging of Parkinson’s disease* A Research Fellow position is available immediately at the Functional Neuroimaging, Cognitive, and Mobility Laboratory, Department of Radiology, University of Michigan, Ann Arbor, MI, USA. Our laboratory specializes in clinical, mobility, cognition, and multimodal neuroimaging studies of Parkinson's disease and is directed by Drs. Nicolaas Bohnen, MD, PhD (Director) and Martijn Muller, PhD (Co-director). We are looking for a post-doctoral candidate to conduct and interpret multimodal and voxel-based imaging analyses of structural, functional MRI and PET datasets to address clinical research questions in patients with Parkinson’s disease. The applicant will also participate in the development of a new neuroimaging and clinical database with incorporated imaging analysis pipeline processing routines. Applicants must have completed a graduate degree (PhD) with relevant experience in multimodal imaging. The applicant must have experience in radiology/radiological sciences, signal processing, functional MRI and diffusion tensor imaging, the use of neuroimaging software packages such as SPM, Freesurfer, Matlab, and FSL. Experience in network-based methods, such as graph theory, would be highly desirable. Additional roles include leadership and active participation in project management activities including the administration of research projects, as well as some teaching sessions and supervision of students. Fluency in English conversation and team work skills to work in a multidisciplinary environment are important. This position will require self-initiative and the ability to work independently without close supervision. Send a brief letter of interest that describes how current skills fit with the required skills for this position, current curriculum vitae, names and contact information of three references to: Dr. Martijn Muller at mtmuller at umich.edu. Compensation of this limited term position will be commensurate with experience and includes health benefits. The University of Michigan is an equal opportunity/affirmative action employer. If applicable, this offer is contingent on your securing valid immigration status and work authorization before your expected start date and maintaining your valid immigration status and work authorization throughout your employment. University of Michigan Health System conducts background screening and pre-employment drug testing on job candidates upon acceptance of a contingent job offer and may use a third party administrator to conduct background screenings. Background screenings are performed in compliance with the Fair Credit Report Act.

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resting state motion censoring
by Adam Martersteck 24 Apr '18

24 Apr '18

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess? If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series? Thanks! Adam

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Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)
by Backhausen, Lea 16 Apr '18

16 Apr '18

Hi Martin, thank you so much for your detailed answer. I will see how we can implement these modifications. Just two quick follow up questions: 1) I have half of the data already processed with the CROSS step using FS 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG steps with FS 6.0.0 or would this corrupt results? 2) Our HPC system is known to have problems from time to time and jobs end up being killed. If the long_submit_jobs job gets killed prematurely would it just resume processing the data that hasn't been processed yet if I submit this job/script again? Thanks again for your help! Best, Lea Backhausen Research assistant Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thursday, February 22, 2018 5:33 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 168, Issue 34 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. Re: Search angle limitation in the flirt registration (Douglas N Greve) 2. Re: Extracting the centroids from Desikan-Killiany atlas (zuxfoucault Wong) 3. Unsubscribe Mailing List (Duy Nguyen) 4. Unknown Label in following postprocessing with mne-python (Daniel van de Velden) 5. Re: Surface Errors (Emily Schwartz) 6. Re: Problem with cortical parcellation of rh but not lh (Amal Achaibou) 7. Re: Longitudinal analysis using SLURM {Disarmed} (Martin Reuter) 8. Re: Longitudinal analysis using SLURM {Disarmed} (Satrajit Ghosh) 9. Re: Longitudinal analysis using SLURM {Disarmed} (Martin Reuter) 10. Re: Freesurfer equivalent to fslmaths? (Bruce Fischl) 11. asymmetric parcellation error (Dijkshoorn, A.B.C. (Aicha)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 21 Feb 2018 18:26:32 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Search angle limitation in the flirt registration To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1e86b3d8-54c6-c9ad-54b3-7cc8df81c5ed(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed you should post your question to the FSL list (they developed and support flirt) On 02/21/2018 05:34 PM, Yixin Ma wrote: > Hi freesurfer developers and users, > > I'm writing to ask about the search angle limitation (--searchrx, -- > searchry and --searchrz) in the flirt function. I use the search angle > option a lot for limited angle search, which usually generate a better > registration result compared with the broad angle search. But I still > don't quite understand how rx,ry and rz are defined and how negative > and positive angles affect the result. Because sometimes I find the > result after the angle limitation does not align well with my > expectation of rotation angle. > > Thank you for your help, > > Yixin Ma > > Brain Image and Analysis Center > > Duke university > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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/ ------------------------------ Message: 2 Date: Thu, 22 Feb 2018 02:23:36 +0000 From: zuxfoucault Wong <zuxfoucault(a)gmail.com> Subject: Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAEUEyJPM6mZ5dSqN6ObDTuBgrEgALr6_USReiwQSHg8K3bW+9g(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Yes! I got better results now! Thanks!! On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker <kw401(a)cam.ac.uk> wrote: > Hi Foucalt, > > I think you need to set the threshold to slightly larger than 0 otherwise > you're taking the center of mass of the whole image (including the 0s) when > really you want to exclude the 0s and only look at the individual regions. > > I changed --thmin 0 to --thmin 0.1 and the results looked good. > > Kx > > On 21 February 2018 at 09:28, zuxfoucault Wong <zuxfoucault(a)gmail.com> > wrote: > >> Attach name file and result file. >> >> Thank you for your time! >> >> Best, >> Foucault >> >> On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong <zuxfoucault(a)gmail.com> >> wrote: >> >>> Hi Kirstie, >>> >>> Thank you very much for the suggestions! >>> I modified my snippet to prevent it from looping the same value and >>> still got the same results? >>> >>> ###### >>> input=($(cat ./names_68parc.txt)) >>> labels=() >>> hemis=() >>> j=0 >>> for i in "${input[@]}"; do >>> if [[ $i == lh_* ]]; then >>> hemis[j]="lh" >>> i=$(echo $i | sed 's/^lh_//g') >>> labels[j]="$i" >>> (( j++ )) >>> elif [[ $i == rh_* ]]; then >>> hemis[j]="rh" >>> i=$(echo $i | sed 's/^rh_//g') >>> labels[j]="$i" >>> (( j++ )) >>> fi >>> done >>> >>> nlabel=68 >>> if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then >>> echo " number of label not match " >>> fi >>> >>> >>> for hemi in lh rh; do >>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels >>> done >>> >>> for ((i=0;i<${#labels[@]};i++)); do >>> mri_surfcluster --in >>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness >>> --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum >>> ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi >>> ${hemis[i]} --subject fsaverage >>> tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut >>> -d' ' -f6-8 >> ./labels/68parc.centroids.txt >>> done >>> ###### >>> >>> >>> The output message of mri_surfcluster: >>> ###### >>> thsign = abs, id = 0 >>> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman >>> Exp $ >>> hemi = rh >>> srcid = >>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness >>> srcsubjid = fsaverage >>> srcsurf = white >>> srcframe = 0 >>> thsign = abs >>> thmin = 0 >>> thmax = -1 >>> fdr = -1 >>> minarea = 0 >>> xfmfile = talairach.xfm >>> clabelfile = ./labels/rh.lateraloccipital.label >>> clabelinv = 0 >>> nth = -1 >>> sumfile = ./labels/sum.rh.lateraloccipital >>> subjectsdir = /usr/local/freesurfer_orig/subjects >>> FixMNI = 1 >>> Loading clabel ./labels/rh.lateraloccipital.label. >>> Found 5963 points in clabel. >>> ------------- XFM matrix (RAS2RAS) --------------- >>> >>> /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm >>> 1.00000 0.00000 0.00000 0.00000; >>> 0.00000 1.00000 0.00000 0.00000; >>> 0.00000 0.00000 1.00000 0.00000; >>> 0.00000 0.00000 0.00000 1.00000; >>> ---------------------------------------------------- >>> Reading source surface >>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white >>> Done reading source surface >>> Computing metric properties >>> Loading source values >>> number of voxels in search space = 5963 >>> Done loading source values (nvtxs = 163842) >>> overall max = 3.19752 at vertex 122846 >>> overall min = 0 at vertex 0 >>> surface nvertices 163842 >>> metric props tot surface area 65020.839844 >>> group_avg_vtxarea_loaded 1 >>> masked surface area 4459.747559 >>> NOT Adjusting threshold for 1-tailed test >>> thminadj = 0 >>> Searching for Clusters ... >>> thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, >>> minarea=0.000000 >>> Found 1 clusters >>> Max cluster size 82167.000000 >>> INFO: fixing MNI talairach coordinates >>> >>> >>> On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker <kw401(a)cam.ac.uk> >>> wrote: >>> >>>> Hi Foucault, >>>> >>>> In the snippet you added you don?t define the labels variable (which >>>> you subsequently loop over in for label in ${labels}). >>>> >>>> There are two possible mistakes that are easy to fix. One may be that >>>> you forgot to read in the labels! And the other is that to get all the >>>> values in an array you need ${labels[@]}. >>>> >>>> I don?t think you need greater precision than you have. The regions are >>>> pretty far apart in mm terms :) >>>> >>>> Kirstie >>>> >>>> Sent from my iPhone, please excuse any typos or excessive brevity >>>> >>>> On 21 Feb 2018, at 03:44, zuxfoucault Wong <zuxfoucault(a)gmail.com> >>>> wrote: >>>> >>>> Dear Freesurfer experts, >>>> >>>> Based on this >>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03333… , I >>>> wrote a short script to extract the centroids from Desikan-Killiany >>>> atlas. >>>> >>>> ###### >>>> for hemi in lh rh; do >>>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir >>>> ./labels >>>> for label in ${labels}; do >>>> mri_surfcluster --in >>>> /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel >>>> ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 >>>> --hemi ${hemi} --subject fsaverage >>>> tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> >>>> ./labels/68parc.centroids.txt >>>> done >>>> done >>>> ####### >>>> >>>> However, 1) the value is not precise enough, it is only one digit after >>>> decimal point. And 2) I kept getting the same value for each hemisphere. >>>> Eg,. >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> >>>> I would appreciate if you have any suggestions regarding extracting >>>> centroids and the aforementioned issues! >>>> Thank you for your time! >>>> >>>> Best, >>>> Foucault >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>> >> >> _______________________________________________ >> 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. >> >> > > > -- > Kirstie Whitaker, PhD > > Research Fellow, Alan Turing Institute > Research Associate, University of Cambridge > > *Mailing Address* > Brain Mapping Unit > Department of Psychiatry > Sir William Hardy Building > Downing Street > Cambridge CB2 3EB > > *Phone: *+44 7583 535 307 <+44%207583%20535307> > *Website:* https://whitakerlab.github.io > *Twitter:* @kirstie_j <https://twitter.com/kirstie_j> > _______________________________________________ > 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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mri_glmfi-sim multi-thread
by Dowling, Kevin Francis 08 Apr '18

08 Apr '18

Dear Freesurfer Experts, My apologies for what might be a very simple question, but I have been unable to locate an answer in the archives/wiki. Our group is trying to cut down on our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, rather than -sim mc-z). I know that --bg will split up the larger number of simulations into n background jobs, but I also noted the warning that this option is not to be used on the Martinos launchpad computational cluster. As we are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is multi-threaded (or can be multi-threaded similar to -parallel flag in recon-all)? We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05) Thank you in advance for your help! Kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215

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Percent Signal Change
by Sarah Cole 03 Apr '18

03 Apr '18

Hi, Could someone please let me know how to get the percent signal change for raw signal intensity? I think the cespct.nii.gz gives me the contrast as %. However, I am not sure about dividing h.nii and h-offset.nii. What are they? Thank you

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Building from source -- autoconf error
by Alle Meije Wink 29 Mar '18

29 Mar '18

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation) After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure I get these messages: rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.… that provided another version of configure.in which might solve the issue. And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac? If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic.

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mri_segment error
by Z Hessam 19 Mar '18

19 Mar '18

Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018 how can i understand why this error happens and what should i do to solve it?

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mir_vol2surface registration file error
by srishti goel 18 Mar '18

18 Mar '18

Hello, We are trying to project a volume map onto a surface. Our network based volume map is a .vmp file and our surface is a nifti file. We were able to convert the volume maps from .vmp to nifti. Our volume map is: negative_allsocial_proportion.nii Our surface is: SN_like_cortical_lh.nii The output file is named: neg_allsocial.nii We are trying to use the following command to now project the volume map on surface and the issues we are facing are: 1) We are unsure of what the purpose of the registration file is and where in the mir_vol2surf command should we specify the surface 2) If it is a matrix for something related to the surface on which we want to project our volume then how should we go about obtaining the registration file appropriate for our comparison. *Command:* mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 *Then to project it:* tksurfer fsaverage lh inflated -ov neg_allsocail.nii

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Freesurfer February 2018