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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Thursday, February 22, 2018 5:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 168, Issue 34 Send Freesurfer mailing list submissions to freesurfer@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-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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 <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Search angle limitation in the flirt registration To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1e86b3d8-54c6-c9ad-54b3-7cc8df81c...@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 <zuxfouca...@gmail.com> Subject: Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <caeueyjpm6mz5dsqn6obdtubgregalr6_usreiwqshg8k3bw...@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 <kw...@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 <zuxfouca...@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 <zuxfouca...@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 <kw...@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 <zuxfouca...@gmail.com> >>>> wrote: >>>> >>>> Dear Freesurfer experts, >>>> >>>> Based on this >>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033337.html >>>> , 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@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@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@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@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. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/919cfd01/attachment-0001.html ------------------------------ Message: 3 Date: Thu, 22 Feb 2018 05:25:14 +0000 From: Duy Nguyen <duy.nguyen...@gmail.com> Subject: [Freesurfer] Unsubscribe Mailing List To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <CAD=uLmRtn=uhirrpefpwlorqodwy6bldd2lvb5p1ghgycuf...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Freesurfer Team Please unsubscribe my email from the list Email: duynguyen....@gmail.com Thanks -- Sent from Iphone -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/efeef7f7/attachment-0001.html ------------------------------ Message: 4 Date: Thu, 22 Feb 2018 14:51:23 +0100 From: Daniel van de Velden <daniel.vandevel...@yahoo.de> Subject: [Freesurfer] Unknown Label in following postprocessing with mne-python To: freesurfer@nmr.mgh.harvard.edu Message-ID: <90db8139-c874-8f56-c426-6e75d4d3c...@yahoo.de> Content-Type: text/plain; charset=utf-8; format=flowed Dear fellow colleagues, in my study I use volumetric source spaces. In the process of creating them, I decided to identify all available volumelabels FreeSurfer "recognized" in the given mri image. Every single subject inherits, despite all other volumelabels, a volumelabel called "Unknown". In an 3D representation of those "unknown" volumelabel coordinates I opine those points could also be part of other volumelabels like cerebral cortex or white matter. Would you please give me a detailed explanation of the origin of this 'Unknown' label? Specifically in respect to the fsaverage "subject". Best regards, Daniel van de Velden ------------------------------ Message: 5 Date: Thu, 22 Feb 2018 13:48:24 +0000 From: Emily Schwartz <emily.schwa...@einstein.yu.edu> Subject: Re: [Freesurfer] Surface Errors To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <86d4b706b0a19c40903668afde4a576c1ec...@aewexcpm21.yuad.uds.yu.edu> Content-Type: text/plain; charset="us-ascii" Hi Doug, Great, thank you. I sent it to you via filedrop. Best, Emily ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Errors yes, filedrop should be find thanks On 02/21/2018 04:44 PM, Emily Schwartz wrote: > Hi Doug, > > I definitely can. I cannot use FTP from this computer for some reason. Can I > upload it via filedrop and should I send it to your email? > > Thanks, > > Emily > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, February 21, 2018 4:29 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Surface Errors > > I'm a little surprised you are getting them so frequently. Can you > upload a couple of subjects so I can take a look? > > > > On 02/21/2018 02:52 PM, Emily Schwartz wrote: >> Hi Doug, >> >> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors >> so often? >> >> Best, >> >> Emily >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Wednesday, February 21, 2018 2:18 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Surface Errors >> >> btw, what verions of FS are you using? >> >> >> On 02/21/2018 01:25 PM, Emily Schwartz wrote: >>> Got it, thank you so much! >>> >>> Best, >>> >>> Emily >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, February 21, 2018 10:23 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Surface Errors >>> >>> Hi Emily >>> >>> it is a segmentation error, but it's a pretty small one. It will mess up >>> the thickness in a region a few mm^2. You could fix it by editing the >>> wm.mgz if you really care about that spot >>> >>> cheers >>> Bruce >>> >>> >>> On Wed, 21 Feb 2018, Emily Schwartz wrote: >>> >>>> Hi Doug, >>>> >>>> Thank you for getting back to me. I've attached two images (Slice165 and >>>> Slice166) with an arrow pointing to the location. I am new at this, so >>>> maybe I am wrong and it is not a segmentation error. >>>> >>>> I've also attached an additional image (Slice185) of what I think is a >>>> type of topological error that I often see multiple times in a subject. Is >>>> this a topological defect? If so, if it is only over 3 slices does it need >>>> to be corrected? >>>> >>>> Thanks again, >>>> >>>> Emily >>>> ________________________________ >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >>>> [gr...@nmr.mgh.harvard.edu] >>>> Sent: Tuesday, February 20, 2018 4:59 PM >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Surface Errors >>>> >>>> sorry, what kind of errors? I could not really tell from the images what >>>> the problem was >>>> >>>> >>>> On 02/20/2018 10:22 AM, Emily Schwartz wrote: >>>>> Hi FreeSurfer community, >>>>> >>>>> I am working on elderly subjects and have had this kind of surface error >>>>> quite often in different locations. Usually, it's over about 3-4 slices >>>>> (in one view) and can be fixed, but I am finding multiple in almost every >>>>> subject and therefore taking a lot of time to edit (and then once >>>>> reprocessed new ones sometimes come up in different locations). I was >>>>> wondering if these are normal to have, minor surface errors that do not >>>>> necessarily need to be fixed. I have added images of an example below. >>>>> Here are some of the values I get from aparc.stats for caudal middle >>>>> frontal lh after manually editing: >>>>> >>>>> Surface area: >>>>> Original - 2500 mm^2 >>>>> Edited - 2532 mm^2 >>>>> >>>>> Grey volume: >>>>> Original - 1710 mm^3 >>>>> Edited - 1727 mm^3 >>>>> >>>>> Thickness avg >>>>> Original - 4455 mm std: 2.371 >>>>> Edited - 4445 mm std: 2.365 >>>>> >>>>> Although the thickness values only differ by 10 mm, we are a little >>>>> concerned because the difference is not within the standard deviation. >>>>> >>>>> Please let me know if all of these errors should be edited or if it may >>>>> be okay to keep the smaller segmentation/topological errors as they are. >>>>> >>>>> Thank you, >>>>> >>>>> Emily >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@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/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@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@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 6 Date: Thu, 22 Feb 2018 14:38:32 +0000 From: Amal Achaibou <amal.achai...@unige.ch> Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <e19056a4047b45d0872bd8697c18c...@unige.ch> Content-Type: text/plain; charset="iso-8859-1" Hi Bruce, I sent you two subject's directories through FileDrop. Thanks! Cheers Amal ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Wednesday, February 21, 2018 6:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh Hi Amal we need the entire directory tree for that subject cheers Bruce On Wed, 21 Feb 2018, Amal Achaibou wrote: > > Hi, > > Yes I've seen it for multiple subjects. > > I'm using version 6. > > Here are the results for one participants, let me know if you need any other > file. > > Thanks > > > Amal > > > > > > > > ____________________________________________________________________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Sent: Thursday, February 15, 2018 8:37 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh > Hi Amal > > this happens for multiple subjects? What version are you using? I have > only ever seen this very rarely and usually for an atypical (e.g. > multiple central sulci) folding pattern. Can you upload a subject so I > can take a look? > > cheers > Bruce > On Tue, 13 Feb 2018, Amal Achaibou wrote: > > > > > Hello, > > > > I'm new to freesurfer and have been trying to use it for cortical > > parcellation of individual T1s > > running recon-all -s subID -i sunT1 -all command. I'm specifically > > interested in getting > > parahippocampal and perirhinal ROIs for each individual. It appears that > > the parcellation is > correct > > for the left hemisphere but not for the right hemisphere... I found that > > there were also > mislabeling > > for precentral and postcentral gyrus (as easy gyri to identify), and that > > regardless of if I > looked > > at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme. > > > > Is there any reason why I have this systematic mistake? Attached is the > > example for one subject > > (others looked very similar). > > > > > > Thanks > > > > > > Amal > > > > > >___________________________________________________________________________________________________ > _ > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/8a3f202f/attachment-0001.html ------------------------------ Message: 7 Date: Thu, 22 Feb 2018 16:43:42 +0100 From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} To: freesurfer@nmr.mgh.harvard.edu Message-ID: <a8423ebe-5055-f8da-b796-a2b291d94...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Hi Lea, I wrote that script to simplify processing on our cluster which uses qsub PBS for submission. I have never used SLURM so far. There is two functions that you (or someone who knows this stuff) would need to modify: def submit and def wait_jobs The submit procedure basically issues a submit command (stored in pbcmd). The examples there should help anyone who programs python to modify it for a slurm submission. The wait_jobs scripts runs a different command (here qstat and grep user) to see how many jobs you are already running and waits until this number sinks below maxjobs, then it continues submitting new jobs. If you don't care about the number of submitted jobs (because your cluster does the scheduling anyway), you can just write " return" as the first line (before the " users = os....." line). Still the submit block would have to be rewritten for slurm. Best, Martin Am 17.02.2018 um 12:13 schrieb Backhausen, Lea: > Dear FS experts, > > I am trying to do a longitudinal analysis of around 250 adolescents > with up to 4 data points each. Given the complexity I would like to > use the long_submit_jobs script which is described here: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts> > > Unfourtunately it does only run on launchpad and I would do the > analyses with SLURM using bash system. > Has anybody adopted the script so i will run with SLURM or does > anybody know where I should look to get information on this? > > I have little scripting experience so any help would be greatly > appreciated! > > Best, > > Lea Backhausen, B.Sc. > > Research assistant > > Klinik und Poliklinik f?r Kinder- und Jugendpsychiatrie und > ?psychotherapie > Tel. +49 (0)351 458-7166 > Fax +49 (0)351 458-5754 > > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 74, 01307 Dresden > *MailScanner has detected a possible fraud attempt from > "deref-web-02.de" claiming to be* _http://www.uniklinikum-dresden.de_ > <https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=http%3A%2F%2Fwww.uniklinikum-dresden.de%2F> > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/1ce21fd2/attachment-0001.html ------------------------------ Message: 8 Date: Thu, 22 Feb 2018 10:48:50 -0500 From: Satrajit Ghosh <sa...@mit.edu> Subject: Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ca+a4womd8kfsqqenav+vtesuna6yujj9p+nfxtzc5-tr7o6...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" hi lea, in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer and then submit each subject's longitudinal pipeline as a separate slurm job. cheers, satra On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu > wrote: > Hi Lea, > > > I wrote that script to simplify processing on our cluster which uses qsub > PBS for submission. I have never used SLURM so far. > > > There is two functions that you (or someone who knows this stuff) would > need to modify: > > def submit > > and > > def wait_jobs > > > The submit procedure basically issues a submit command (stored in pbcmd). > The examples there should help anyone who programs python to modify it for > a slurm submission. > > > The wait_jobs scripts runs a different command (here qstat and grep user) > to see how many jobs you are already running and waits until this number > sinks below maxjobs, then it continues submitting new jobs. If you don't > care about the number of submitted jobs (because your cluster does the > scheduling anyway), you can just write > > > " return" as the first line (before the " users = os....." line). > > > Still the submit block would have to be rewritten for slurm. > > > Best, Martin > > > > Am 17.02.2018 um 12:13 schrieb Backhausen, Lea: > > Dear FS experts, > > I am trying to do a longitudinal analysis of around 250 adolescents with > up to 4 data points each. Given the complexity I would like to use the > long_submit_jobs script which is described here: https://surfer.nmr.mgh. > harvard.edu/fswiki/FsTutorial/Scripts > > Unfourtunately it does only run on launchpad and I would do the analyses > with SLURM using bash system. > Has anybody adopted the script so i will run with SLURM or does anybody > know where I should look to get information on this? > > I have little scripting experience so any help would be greatly > appreciated! > > Best, > > Lea Backhausen, B.Sc. > > Research assistant > > Klinik und Poliklinik f?r Kinder- und Jugendpsychiatrie und ?psychotherapie > Tel. +49 (0)351 458-7166 <+49%20351%204587166> > Fax +49 (0)351 458-5754 <+49%20351%204585754> > > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 74, 01307 Dresden > *MailScanner has detected a possible fraud attempt from "deref-web-02.de" > claiming to be* *http://www.uniklinikum-dresden.de* > <https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=http%3A%2F%2Fwww.uniklinikum-dresden.de%2F> > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/c4c61c6f/attachment-0001.html ------------------------------ Message: 9 Date: Thu, 22 Feb 2018 17:07:36 +0100 From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} To: freesurfer@nmr.mgh.harvard.edu Message-ID: <55525bba-9a6a-214f-bcc6-4d3b1267c...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Could be all that is needed is to add this: mycluster ='sbatch --mail-type=FAIL --mail-user=<typeyouremailhere> -N 1 --ntasks-per-node=10 --partition=work --export=ALL -o <pathtohomes>/%(username)s/logs/job.%J.out- e <pathtohomes>/%(username)/logs/job.%J.err "%(command)s"' and comment the lines # if queue is not None ... # pbcmd = ... with a hashtag. you can also simplify the slurm command (remove the --mail flags and the -o logfile location flags) your cluster partition may not be called "work" either. Best, Martin Am 22.02.2018 um 16:43 schrieb Martin Reuter: > > Hi Lea, > > > I wrote that script to simplify processing on our cluster which uses > qsub PBS for submission. I have never used SLURM so far. > > > There is two functions that you (or someone who knows this stuff) > would need to modify: > > def submit > > and > > def wait_jobs > > > The submit procedure basically issues a submit command (stored in > pbcmd). The examples there should help anyone who programs python to > modify it for a slurm submission. > > > The wait_jobs scripts runs a different command (here qstat and grep > user) to see how many jobs you are already running and waits until > this number sinks below maxjobs, then it continues submitting new > jobs. If you don't care about the number of submitted jobs (because > your cluster does the scheduling anyway), you can just write > > > " return" as the first line (before the " users = os....." line). > > > Still the submit block would have to be rewritten for slurm. > > > Best, Martin > > > > Am 17.02.2018 um 12:13 schrieb Backhausen, Lea: >> Dear FS experts, >> >> I am trying to do a longitudinal analysis of around 250 adolescents >> with up to 4 data points each. Given the complexity I would like to >> use the long_submit_jobs script which is described here: >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts >> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts> >> >> Unfourtunately it does only run on launchpad and I would do the >> analyses with SLURM using bash system. >> Has anybody adopted the script so i will run with SLURM or does >> anybody know where I should look to get information on this? >> >> I have little scripting experience so any help would be greatly >> appreciated! >> >> Best, >> >> Lea Backhausen, B.Sc. >> >> Research assistant >> >> Klinik und Poliklinik f?r Kinder- und Jugendpsychiatrie und >> ?psychotherapie >> Tel. +49 (0)351 458-7166 >> Fax +49 (0)351 458-5754 >> >> Universit?tsklinikum Carl Gustav Carus >> an der Technischen Universit?t Dresden >> Anstalt des ?ffentlichen Rechts des Freistaates Sachsen >> Fetscherstra?e 74, 01307 Dresden >> *MailScanner has detected a possible fraud attempt from >> "deref-web-02.de" claiming to be* _http://www.uniklinikum-dresden.de_ >> <https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=http%3A%2F%2Fwww.uniklinikum-dresden.de%2F> >> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer >> Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba >> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/dfc97f5a/attachment-0001.html ------------------------------ Message: 10 Date: Thu, 22 Feb 2018 11:10:42 -0500 (EST) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer equivalent to fslmaths? To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1802221110230.11...@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Jared what are the exact command lines you ran? I don't think it can be a freeview problem if the overlays are different. cheers Bruce On Wed, 21 Feb 2018, Zimmerman, Jared wrote: > > Hey Doug, Bruce, et al., any update on why fscalc and Matlab are not > producing the same values when > trying to run a mean?? I?m using fscalc to pilot some stuff now, but not sure > if I should be > trusting the values I?m getting out of it. > > ? > > It seems this issue might be caused by how Freeview is reading the images and > not by either Matlab > or fscalc.? See the screenshot below.? The two overlays loaded in Freeview > should be the exact same > image, which is the mean of three other images, one calculated with fscalc > (*smMean246.mgh) and the > other by reading the images into Matlab (*matlab_lh.mgh).? Notice that at the > crosshair (vertex > 37431) the values in the two overlays are different by ~0.03, or ~3.5%.? > > ? > > However, if I read these two images into Matlab with MRIread() and look at > that vertex, both images > have the same value, which is 1.9042 > > ? > > So it seems like maybe Freeview and Matlab are not reporting the same values > for the images, and > possibly the images I write in Matlab are somehow getting depressed by > Freeview.? I?m not able to > stay connected to my cluster for much longer than 10-15 min at the moment, so > it?s hard for me to > troubleshoot more, but I can provide sample images and code to recreate the > problem tomorrow. > > ? > > Is this a known issue that somehow images written in Matlab are not read > properly by Freeview? > > ? > > This is on v5.3.0 and Matlab 2014b.? I can try tomorrow if the issue persists > in v6.0 > > ? > > Thanks, > > Jared > > ? > > ? > > ? > > [IMAGE] > > ? > > ? > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Zimmerman, Jared" > <jar...@pennmedicine.upenn.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Friday, February 16, 2018 at 2:12 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer equivalent to fslmaths? > > ? > > Thanks Doug and Bruce,? > > ? > > Fscalc is great because I can do maths with multiple inputs, like a mean.? > I?m noticing, however, > that when I do a mean with fscalc I get different values than when I do the > mean in Matlab, any idea > why?? In some regions the differences are as much as 5-10% so I don?t think > it?s just a > rounding/precision issue. > > ? > > fscalc a.mgh add b.mgh add c.mgh add d.mgh add e.mgh div 5 --odt float --o > mean.mgh > > ? > > Hard to imagine it?s an order of operations issue, but I am a little confused > about how fscalc > handles order of operations from the help page. > > ? > > I?m using v5.3.0 and Matlab 2014b > > ? > > Thanks, > > Jared > > ? > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <gr...@nmr.mgh.harvard.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Friday, February 16, 2018 at 11:31 AM > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer equivalent to fslmaths? > > ? > > Or fscalc > > ? > > On 2/16/18 11:22 AM, Bruce Fischl wrote: > > Hi Jared > > I think mris_calc does at least some of what you want. > > cheers > Bruce > On Fri, 16 Feb 2018, Zimmerman, Jared wrote: > > > > > Hi all, > > ? > > Is there an equivalent of fslmaths in Freesurfer?? I would like > to add two > scalar value images (.mgh > files) that are registered to the fsaverage6 surface but I?m not > seeing an > obvious way to do it.? > Right now I?m reading the images into Matlab to add them, but > this is a bit > inconvenient because > what I would like to do is smooth an image by a small amount, add > the > original image back to it, > then smooth again marginally and iterate until I get to a target > fwhm.? > Since I can?t smooth inside > Matlab this necessitates writing out a temp image for each > smoothing step > then reading it back into > Matlab for the adding.? Obviously this is a solvable problem, but > as someone > only marginally > proficient in Matlab it?s something I?d like to avoid, plus it > seems like a > lot of I/O for this > task. > > ? > > A little more detail on my data and what I?m trying to do: > > ? > > The scalar images I?m working with are network confidence maps, > basically > like the spatial maps from > an ICA dual-regression.? I want to combine the confidence maps > together into > a hard partition and > write it to an annot file, but I want to smooth them first.? I?m > concerned, > however, that smoothing > is going to bias the parcellation against small network parcels > and in favor > of large network > parcels because in each confidence map the small parcels will be > surrounded > by lots of zeros (does > this make sense?).? To correct for this, my idea was to > iteratively smooth > by small amounts and to > add the original confidence values (or some fraction of them) > back to the > smoothed map after each > iteration so that regions of high confidence with a small/narrow > spatial > spread do not become > diluted by the smoothing and don?t get taken over by larger high > confidence > regions in nearby > networks. > > ? > > One final question would be how to smooth on a surface without > resampling.? > Right now I?m using > mri_surf2surf and smoothing when I resample to the native mesh, > but if I > take the above approach I > would not want to resample at each smoothing step.? Could I just > use > mri_surf2surf with ?srcsubject > and ?trgsubject pointing to the same subject? > > ? > > ? > > Thanks, > > Jared > > ____________________________ > > Jared P. Zimmerman > > jar...@pennmedicine.upenn.edu > > Neuroscience Graduate Student > > Oathes Lab > > University of Pennsylvania > > ? > > ? > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ------------------------------ Message: 11 Date: Thu, 22 Feb 2018 16:32:58 +0000 From: "Dijkshoorn, A.B.C. (Aicha)" <a.b.c.dijksho...@uu.nl> Subject: [Freesurfer] asymmetric parcellation error To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <5fb4d2a0ecbd934b877c8b9c3d94c78805f52...@wp0046.soliscom.uu.nl> Content-Type: text/plain; charset="iso-8859-1" Dear Freesurfer developers, When I was troubleshooting my data I came across an odd parcellation error that I can not place. When looking at the reconstructed surface parcellation (freeview -f {$subject}/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ --viewport 3d) I noticed that in a large proportion of my subjects the parcellated errors are not placed correctly. Moreover, the error mostly seems to apply to the right cortex and not the left. I adjusted foto's for visual information. Do you have any idea what could have gone wrong and how I can correct for this? Kind regards, Aicha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180222/6dc4c15b/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... 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