[Freesurfer] Makefile for Tracula
External Email - Use Caution Hi everyone! Firstly - and most importantly - thank you for the awesome tool, and for all your help in using it! I'm re-processing (and re-quality controll-ing) data that was formatted in v5.3 into v6 and I've come to re-running trac-all. I've been using v6 with the updated Makefile (if anyone's googling this question, see the note at this page about the fact that v6 doesn't ship with the correct make file https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0#Tipsandgeneralquestions ). I wonder if a) there is a makefile for trac-all (that would be amazing) or b) you could tell me which files I need to delete so I re-process them now that the surfaces are updated? I assume the DTI processing hasn't changed, so I shouldn't need to change the bedpostx folder for example, but I'm not 100% sure on which other files have dependences on the reconstructions :) (The surfaces got pretty messed up in this update so I'd like to go back to basicswithout having to rerun things we KNOW aren't related to the surface reconstructions.) Thank you! Kirstie -- 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 *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
Re: [Freesurfer] Version 6.0.0 or 6.0.1?
External Email - Use Caution Thank you for clarifying. One big problem was the error in the make file and I think I'm still somewhat suffering from that even though I've replaced the file. The short answer is that if I run recon-all -make all on the same subject twice it will re-run recon-all on that second occasion...I don't know why make isn't detecting that I had just run the command! (There must be an error - it's just strange that it happens on approx 5% of all my scans but in no discernable way!) The main thing I'm trying to do is move from 5.3 to 6.0 processing while keeping the quality control edits that we've spent a lot of time on. We have quantitative R1 maps which means recon-all isn't tuned for the maps and we've done a lot of rounds of manual edits that I don't want to lose! So if anyone knows exactly which files should be copied across to a new folder from our 5.3 backup that will allow 6.0 to run recon-all but still put the surfaces in around about the same place that would be great :) I don't think this will be fixed with 6.0.1! Thank you for clarifying :) Kx On Tue, 11 Dec 2018 at 18:36, Hoopes, Andrew wrote: > Hi Kirstie, sorry for the lack of documentation – there’s practically no > difference between 6.0.0 and 6.0.1. The only update in 6.0.1 is the ability > to point to an external license using the FS_LICENSE environment variable. > What kind of issues are you having with 6.0.0? > > > > Best, > > Andrew > > > > > > *From: * on behalf of Kirstie > Whitaker > *Reply-To: *FS Help > *Date: *Tuesday, December 11, 2018 at 4:28 AM > *To: *FS Help > *Subject: *[Freesurfer] Version 6.0.0 or 6.0.1? > > > > *External Email - Use Caution* > > Hi Freesurfer team, > > > > On the download website version 6.0.0 is linked: > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > > > But on this list there has been discussion of version 6.0.1 which can be > downloaded from > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1 > > > > What's the recommended version to use? > > > > I've been using 6.0.0 but with an updated make file following the > instructions in this email: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.html > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-April/056644.html> > > > > Is the makefile updated in 6.0.1? Are there any other differences? I'm > having a lot of difficulty getting recon-all to run reliably with 6.0.0 > (some subjects are fine, others not!) and I'm wondering if that's because > I'm supposed to be using 6.0.1? > > > > Thank you for your help! > > Kirstie > > > > -- > > 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 > > *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 -- 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 *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
[Freesurfer] Version 6.0.0 or 6.0.1?
External Email - Use Caution Hi Freesurfer team, On the download website version 6.0.0 is linked: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall But on this list there has been discussion of version 6.0.1 which can be downloaded from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1 What's the recommended version to use? I've been using 6.0.0 but with an updated make file following the instructions in this email: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.html Is the makefile updated in 6.0.1? Are there any other differences? I'm having a lot of difficulty getting recon-all to run reliably with 6.0.0 (some subjects are fine, others not!) and I'm wondering if that's because I'm supposed to be using 6.0.1? Thank you for your help! Kirstie -- 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 *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
Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas
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/sub >> jects/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/sub >> jects/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 >> 1.0 0.0 0.0 0.0; >> 0.0 1.0 0.0 0.0; >> 0.0 0.0 1.0 0.0; >> 0.0 0.0 0.0 1.0; >> >> Reading source surface /usr/local/freesurfer_orig/sub >> jects/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=0.00 (0.00), thmax=-1.00 (-1), thsignid=0, >> minarea=0.00 >> Found 1 clusters >> Max cluster size 82167.00 >> 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
Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas
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 Wongwrote: > > Dear Freesurfer experts, > > Based on this > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/07.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.
Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing
Hi freesurfer team, I just ran into this error. I fixed it by switching from python 3.6 to python 2.7. Does this sound like the right fix? I wonder if it is documented somewhere on the wiki? Thank you for the great tool! Kx On 18 November 2016 at 21:14, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > what happens when you run asegstats2table --help > > It does not fail for me. I wonder if it is a python version problem > > > On 11/18/2016 04:01 PM, Elijah Mak wrote: > > Hi ZK, > > > > Thanks. It is great news! I would like to report the following. > > > > asegstats2table seems to be acting strangely. > > > > File "/Applications/freesurfer_b6/bin/asegstats2table", line 195 > > > > print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' > > > > Even typing asegstats2table --help leads to the same error message. > > It was not found in a prev dev built or in 5.3. > > > > Thanks. > > > > Also, not sure if it's placebo, but freeview seems to be running > > quicker now. > > > > Best Wishes, > > > > Elijah > > > > > > > > > > ___ > > 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. > > -- Kirstie Whitaker, PhD Mozilla Fellow for Science <https://science.mozilla.org/programs/fellowships> Postdoctoral researcher Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com *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.
Re: [Freesurfer] Quality control with different pipelines
Brilliant - many thanks. Kx On 22 June 2016 at 14:57, Harms, Michael <mha...@wustl.edu> wrote: > > Yes on all fronts. > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie > Whitaker <kw...@cam.ac.uk> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Wednesday, June 22, 2016 at 8:55 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Quality control with different pipelines > > Thank you Michael! > > So - just to be super sure I'm on the same page here. If I've run a > subject using 5.3 I take that same subject directory (after backing it up > somewhere) and then run the dev version of recon-all with the -all flag. > After it's completed I (should - contingent on checking again as you > recommend) have a well edited subject who can now be reported as having > been processed with the dev version, right? > > Thanks again > Kx > > On 22 June 2016 at 14:48, Harms, Michael <mha...@wustl.edu> wrote: > >> >> Hi, >> You can simply rerun 'recon-all -all’ on top of your already >> processed/edited subject, and it will respect your previous edits. Of >> course, it is a good idea to still review/QC the results afterwards, to >> make sure that the outcome of those edits is satisfactory under the new FS >> version. >> >> And, if you want to preserve your results under FS 5.3, then you should >> make a copy of those results before rerunning recon-all. >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: mha...@wustl.edu >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie >> Whitaker <kw...@cam.ac.uk> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Date: Wednesday, June 22, 2016 at 1:28 AM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: [Freesurfer] Quality control with different pipelines >> >> Hi everyone, >> >> I processed and edited 300 participants for our study using Freesurfer >> 5.3 and I'd like to move to using the dev version that's currently >> available because we have a bunch more data that's been collected and I >> think it does a better job. (This question also applies to moving to v 6 >> when it is released). >> >> If I run the dev version of recon-all and then copy over the control >> points and wm.mgz files that we edited in the original run, and run >> recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very >> good approximation for the edits we conducted? Or does this "shortcut" not >> do what I think it does? >> >> Does anyone have any experience moving from one version of freesurfer to >> another without having to start from square one with the edits? >> >> Thank you again for the fantastic tools! >> >> Kx >> >> >> -- >> Kirstie Whitaker, PhD >> Research Associate >> >> Department of Psychiatry >> 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 >> *Website:* www.kirstiewhitaker.com >> >> >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/
Re: [Freesurfer] Quality control with different pipelines
Thank you Michael! So - just to be super sure I'm on the same page here. If I've run a subject using 5.3 I take that same subject directory (after backing it up somewhere) and then run the dev version of recon-all with the -all flag. After it's completed I (should - contingent on checking again as you recommend) have a well edited subject who can now be reported as having been processed with the dev version, right? Thanks again Kx On 22 June 2016 at 14:48, Harms, Michael <mha...@wustl.edu> wrote: > > Hi, > You can simply rerun 'recon-all -all’ on top of your already > processed/edited subject, and it will respect your previous edits. Of > course, it is a good idea to still review/QC the results afterwards, to > make sure that the outcome of those edits is satisfactory under the new FS > version. > > And, if you want to preserve your results under FS 5.3, then you should > make a copy of those results before rerunning recon-all. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie > Whitaker <kw...@cam.ac.uk> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Wednesday, June 22, 2016 at 1:28 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] Quality control with different pipelines > > Hi everyone, > > I processed and edited 300 participants for our study using Freesurfer 5.3 > and I'd like to move to using the dev version that's currently available > because we have a bunch more data that's been collected and I think it does > a better job. (This question also applies to moving to v 6 when it is > released). > > If I run the dev version of recon-all and then copy over the control > points and wm.mgz files that we edited in the original run, and run > recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very > good approximation for the edits we conducted? Or does this "shortcut" not > do what I think it does? > > Does anyone have any experience moving from one version of freesurfer to > another without having to start from square one with the edits? > > Thank you again for the fantastic tools! > > Kx > > > -- > Kirstie Whitaker, PhD > Research Associate > > Department of Psychiatry > 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 > *Website:* www.kirstiewhitaker.com > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return 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 Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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] Quality control with different pipelines
Hi everyone, I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released). If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does? Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits? Thank you again for the fantastic tools! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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] Accuracy of D-K atlas for different age ranges
Hi Freesurfer community, A reviewer has asked how accurate the application of freesurfer regional labels are to different age ranges (specifically our study is between 14 and 24 years old). I'm sure this question has been answered elsewhere so please do forgive me for being lazy and simply asking you to recommend good references rather than searching for them in PubMed! Thank you! Kirstie x -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] Visualising regional values on the surface
Brilliant - I think that's probably my friend! Thanks again everyone for all the help! Kx On 29 March 2016 at 16:50, Michael Waskom <mwas...@stanford.edu> wrote: > Hi Kirstie, > > Nibabel has a write_annot function that should work: > http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#write-annot > > Best, > Michael > > On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker <kw...@cam.ac.uk> wrote: > >> Thank you Michael! I <3 Pysurfer. >> >> (and freesurfer of course!) >> >> The *real* goal is to integrate the code that I've written as a wrapper >> around pysurfer to show regional values (exactly as you suggest) with >> BrainNet <https://www.nitrc.org/projects/bnv/> which can show the >> network nicely on top of freesurfer files. >> >> Here's the wiki for my pysurfer wrapper: >> https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-with-Pysurfer >> >> And the code itself >> https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py >> >> Unfortunately I don't use BrainNet so I'm having difficulty helping my >> lab mate make his pretty plots of network nodes and edges overlayed on top >> of surface colors (eg: modular partition)! >> >> Is there a way of writing out an annot file from pysurfer into freesurfer >> format? Maybe that would bring the two packages closer together >> >> Kx >> >> >> >> >> >> On 29 March 2016 at 16:29, Michael Waskom <mwas...@stanford.edu> wrote: >> >>> Hi Kirstie, >>> >>> Here's an example of how to do this in PySurfer: >>> http://pysurfer.github.io/examples/plot_parc_values.html >>> >>> Hope that helps, >>> Michael >>> >>> On Tue, Mar 29, 2016 at 8:08 AM, dgw <dgwake...@gmail.com> wrote: >>> >>>> Hi Kirstie, >>>> >>>> You could write your own CLUT file with the color corresponding to the >>>> correlation you want to show? >>>> Just open up the file and play with the values in the color columns. >>>> Then simply load the color table in Freeview and use it to visualize >>>> the annotation. >>>> >>>> There are of course other ways, but this is probably the quickest. >>>> >>>> hth >>>> d >>>> >>>> >>>> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker <kw...@cam.ac.uk> >>>> wrote: >>>> > Hi, >>>> > >>>> > I'd like to show correlation coefficients by region on the brain >>>> surface. So >>>> > for example, if I've calculated a modular decomposition in a network >>>> > analysis for each region of the D-K atlas I'd like to be able to >>>> color each >>>> > atlas region according to the module it has been assigned to. >>>> > >>>> > It seems like I have to do something with the ?h.aparc.annot files >>>> and a >>>> > colour lookup table but I'm not sure exactly what. >>>> > >>>> > Thank you! >>>> > Kx >>>> > >>>> > -- >>>> > Kirstie Whitaker, PhD >>>> > Research Associate >>>> > >>>> > Department of Psychiatry >>>> > 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 >>>> > Website: www.kirstiewhitaker.com >>>> > >>>> > ___ >>>> > 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 >&g
Re: [Freesurfer] Visualising regional values on the surface
Thank you Michael! I <3 Pysurfer. (and freesurfer of course!) The *real* goal is to integrate the code that I've written as a wrapper around pysurfer to show regional values (exactly as you suggest) with BrainNet <https://www.nitrc.org/projects/bnv/> which can show the network nicely on top of freesurfer files. Here's the wiki for my pysurfer wrapper: https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-with-Pysurfer And the code itself https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py Unfortunately I don't use BrainNet so I'm having difficulty helping my lab mate make his pretty plots of network nodes and edges overlayed on top of surface colors (eg: modular partition)! Is there a way of writing out an annot file from pysurfer into freesurfer format? Maybe that would bring the two packages closer together Kx On 29 March 2016 at 16:29, Michael Waskom <mwas...@stanford.edu> wrote: > Hi Kirstie, > > Here's an example of how to do this in PySurfer: > http://pysurfer.github.io/examples/plot_parc_values.html > > Hope that helps, > Michael > > On Tue, Mar 29, 2016 at 8:08 AM, dgw <dgwake...@gmail.com> wrote: > >> Hi Kirstie, >> >> You could write your own CLUT file with the color corresponding to the >> correlation you want to show? >> Just open up the file and play with the values in the color columns. >> Then simply load the color table in Freeview and use it to visualize >> the annotation. >> >> There are of course other ways, but this is probably the quickest. >> >> hth >> d >> >> >> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker <kw...@cam.ac.uk> >> wrote: >> > Hi, >> > >> > I'd like to show correlation coefficients by region on the brain >> surface. So >> > for example, if I've calculated a modular decomposition in a network >> > analysis for each region of the D-K atlas I'd like to be able to color >> each >> > atlas region according to the module it has been assigned to. >> > >> > It seems like I have to do something with the ?h.aparc.annot files and a >> > colour lookup table but I'm not sure exactly what. >> > >> > Thank you! >> > Kx >> > >> > -- >> > Kirstie Whitaker, PhD >> > Research Associate >> > >> > Department of Psychiatry >> > 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 >> > Website: www.kirstiewhitaker.com >> > >> > ___ >> > 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 > > > 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 Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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] Visualising regional values on the surface
Hi, I'd like to show correlation coefficients by region on the brain surface. So for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color each atlas region according to the module it has been assigned to. It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what. Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] FA and MD *positively* correlated within same regions ?
I think eroding the region makes sense in general - you just have to be careful to exclude subjects who end up with no data (as you discovered!) You could also look into why these three subjects had such small wm regions under entorhinal cortex. My (still) suspicious mind wonders if there is a bad reconstruction that is cutting out part of the inferior temporal lobe and therefore "squeezing" all of the cortical labels into a smaller volume. This would in turn give very small wm volumes. On the other hand, entorhinal cortex may just have a relatively small amount of white matter underlying it because it's so "narrow" such that when you erode by 1mm you are left with nothing for these three subjects. Glad you figured out the odd correlations! Kx Sent from my iPhone, please excuse any typos or excessive brevity > On 25 Mar 2016, at 01:22, Elijah Makwrote: > > Hi Kirstie, > > Yes indeed there were 3 subjects at the bottom-left of the plot. > > To account for PV, I eroded the boundaries using -seg-erode 1 during the > mri_segstats stage, and this resulted in a few subjects with no data for the > WM entorhinal region (although these were saved as "0" in the .stats file). > Do people generally do this for DTI studies? > > All good now. > > Many thanks again, Kirstie. > > Best Wishes, > Elijah > > > ___ > 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.
Re: [Freesurfer] FA and MD *positively* correlated within same regions ?
Hi Elijah, Is there any chance you could attach a scatter plot? My suspicious mind thinks either a) there are outliers who are doing odd things, or b) the FA values are very different to those in other regions and therefore the correlation with MD wouldn't be expected to be the same. Kx Sent from my iPhone, please excuse any typos or excessive brevity > On 24 Mar 2016, at 23:59, Elijah Makwrote: > > Hi Alshikho, > > Yes, I am sure :) Same sequence for everyone. > > Just to add. FA and MD were significantly negatively correlated for the other > regions including the fusiform, precuneus, hippocampus, thalamus, etc. > > So I am very curious about what could be going on with the ERC here? > > Best Wishes, > Elijah > > ___ > 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] Postdoc job: Neuroimaging of mood disorders in adolescence at University of Cambridge
Dear FSL, Freesurfer and Neuroimaging in Python list members (with apologies for cross posting), The closing date for this position is this SUNDAY 20th MARCH, so you don't have much time (although we only need a cover letter and CV type details for your application), but I've been asked to reach out to you because we'd really like to hire the very best postdoc for this role at the University of Cambridge. Please share this email widely with your personal and professional networks. The successful applicant will join a multidisciplinary team of scientists investigating the neural basis and cognitive correlates of behavioural phenotypes in large existing and still being collected longitudinal community and clinical cohorts of adolescents and young adults as part of the Neuroscience in Psychiatry Network (http://nspn.org.uk). Applicants will have a PhD and some postdoctoral experience reflecting an expert level of knowledge in cognitive and behavioural neuroscience together with a working knowledge and interest in longitudinal data analysis and mental illness. The full job advert and instructions on how to apply are at http://www.jobs.cam.ac.uk/job/9696. The role comes with an invitation to interview for a fellowship at Peterhouse, the oldest remaining college in Cambridge. The start date is (reasonably) flexible but projected for May 2016. The funds for this post are available until 31 March 2018 in the first instance. The Clinical School at the University of Cambridge is a proud holder of an Athena SWAN Silver award <http://athena-swan.medschl.cam.ac.uk/> and candidates from groups that are under-represented in senior STEMM positions (such as women and people of colour) are particularly encouraged to apply. If you have any informal questions about this vacancy please contact Professor Ian Goodyer (ig...@cam.ac.uk) For information on the application process for this vacancy, please contact Dominic Drane, HR Administrator via email on hradminpsychia...@medschl.cam.ac.uk. Please quote reference RN08523 on your application and in any correspondence about this vacancy. Thank you Kirstie Whitaker -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] group mean greater than X
Could you also just subtract 5 from all your input data? Then when you test against zero (and only look at positive p values) you'll really be testing whether the values are greater than 5? Kx On 11 November 2015 at 21:35, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > I guess you could subtract 5 from the gamma.mgh, then recompute the t = > gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p > or sig given the dof. > doug > > ps. Please remember to include previous correspondences so we know the > context of the question > > On 11/11/15 4:10 PM, Dace Apshvalka wrote: > > Sorry, I was not very clear. > > > > I meant, how do I test whether the group mean is greater than 5, for > > example. > > > > The default is 0, but can I change it somehow? > > > > > > Dace > > ___ > 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 Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] Visualising surfaces at different fractional depths
Thank you - right as you sent your reply I was writing an apology because I'd just seen that flag. It's Friday evening here in the UK and it might be time to stop sending emails for a little while! So sorry! And thank you! Kx On 24 April 2015 at 18:33, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can pick the interpolation method with --interp string where string is one of: nearest trilinear sinc cubic cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see a section that describes exactly how the values are interpolated (if they're interploated) onto the surface. The assumption that I was trying to clarify in my (too short) email was that the voxel through which the vertex passes is the value that is mapped to that vertex. Possible alternatives would be some sort of weighted sum of the neighboring voxels, perhaps, but I had assumed that if there were interpolations happening it would be mentioned in the help file? Does this make sense? I do apologise if I've missed an obvious reference that explains all this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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
Re: [Freesurfer] Visualising surfaces at different fractional depths
Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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 Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] Visualising surfaces at different fractional depths
I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see a section that describes exactly how the values are interpolated (if they're interploated) onto the surface. The assumption that I was trying to clarify in my (too short) email was that the voxel through which the vertex passes is the value that is mapped to that vertex. Possible alternatives would be some sort of weighted sum of the neighboring voxels, perhaps, but I had assumed that if there were interpolations happening it would be mentioned in the help file? Does this make sense? I do apologise if I've missed an obvious reference that explains all this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks again for the help! Kx On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kirstie you can do this with mris_expand. For example: mris_expand -thickness lh.white 0.5 lh.graymid will generate a surface halfway between white and pial. Using that surface to sample is probably a better method than using profrac, although I expect the differences will be small unless you have very highres data. cheers Bruce On Mon, 20 Apr 2015, Kirstie Whitaker wrote: Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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 Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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 Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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
[Freesurfer] Visualising surfaces at different fractional depths
Hi experts, I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a volume halfway between the pial and white matter surfaces. I was wondering if there was a way to visualise where this surface lay on the volume? Ideally I'd like to show a figure with the pial, white and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface
Thank you, Doug. Can I just check that projdist is the same as projabs but with a different name? Just in case I'm using an old/wrong version, here's the last line from the mri_vol2surf help output: $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $ From that help and your email I'm looking to run: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh Which will give me values that are 2mm toward white matter from the pial surface. Thanks again for all the help! Kx On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can spec the surface to be pial (instead of the default white). Then spec --projabs to specify the distance into cortex (using negative numbers). doug On 11/27/14 1:24 PM, Kirstie Whitaker wrote: Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface
Sorry - if anyone's looking at this in the future, you also need --regheader subID in the command: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh \ --regheader subid Kx On 4 December 2014 at 20:41, Kirstie Whitaker kw...@cam.ac.uk wrote: Thank you, Doug. Can I just check that projdist is the same as projabs but with a different name? Just in case I'm using an old/wrong version, here's the last line from the mri_vol2surf help output: $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $ From that help and your email I'm looking to run: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh Which will give me values that are 2mm toward white matter from the pial surface. Thanks again for all the help! Kx On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can spec the surface to be pial (instead of the default white). Then spec --projabs to specify the distance into cortex (using negative numbers). doug On 11/27/14 1:24 PM, Kirstie Whitaker wrote: Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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] mri_vol2surf --prodist measuring from pial surface
Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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] Appropriate levels of surface smoothing
Hi everyone, Firstly - thank you for the excellent tools. This year has been my first foray into surfaced based analysis and I'm enjoying it very much. I don't currently have a gut instinct for an appropriate level of surface smoothing. I'm sure that can't be easily answered but would a range of, say, 3 to 5mm sound good? Or more like 10 to 15mm? Currently I'm considering cortical thickness analyses, but I may extend into functional analyses in the future. If there are any references that you can recommend I'd appreciate that very much. Best wishes Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 *Website:* www.kirstiewhitaker.com ___ 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] tracula update link not working
Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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.
Re: [Freesurfer] tracula update link not working
Yep! Working now - thank you very much :) Kx On 20 August 2014 12:23, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Kirstie - This was a glitch related to yesterday's storage cluster maintence. It's been fixed now, so please try again. a.y On Wed, 20 Aug 2014, Kirstie Whitaker wrote: Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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 Associate Department of Psychiatry 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 Website: www.kirstiewhitaker.com ___ 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] Some notes on getting Tracula to work for newbies
Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!) [Note that if I've written something between then it will be specific to your files/directories etc] When running trac-all on an input nii file with corresponding bval and bvec files: 1) If you're getting an error that says: nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI NIFTI FILE Try running the command: fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE eg: fslmaths dti.nii.gz dti.nii.gz I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me. 2) If you're getting an error that says ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well. To install the update just download it (I used wget TRACULA_UPDATE_LINK) and the untar it (tar -zxvf TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory. 3) If you're getting an error that says (something along the lines of) mri_convert --frame 0 14 27 41 54 68 SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz mri_convert: extra arguments (41 and following) type mri_convert -u for usage Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 2). Some fun facts from my experience: You can have decimal points (not commas though) in your bvals files. You can run trac-all in either a bash or tcsh shell. (These were not the droids I was looking for) Thanks again for the really excellent software. And please correct anything that I've written here if it's wrong! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Some notes on getting Tracula to work for newbies
On 20 August 2014 14:27, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You are a model user :) Thank youalthough unfortunately not quite the best user - I still have problems... I think I lied in my earlier email - I think that the mri_convert problem (#3 below) is actually in the newest version of trac-preproc. (I didn't do a great job of keeping track of my version because I was being lazy! More fool me.) Here's the part of the code which in the May 2014 update ('$Id: trac-preproc,v 1.49 2014/03/22 03:31:22 ayendiki Exp $' ) that is leading to the error: #= # Make diffusion brain mask if ($#nb0 0) then set lowblist = () @ k = 0 while ($k $nb0) set lowblist = ($lowblist $k) @ k = $k + 1 end else set bmin = `grep -v ^$ $dwidir/dwi_orig.mghdti.bvals \ | sort --numeric-sort | head -1` set lowblist = `cat $dwidir/dwi_orig.mghdti.bvals \ | awk -v bmin=$bmin '{if ($1 == bmin) print NR-1}'` endif if (! $#lowblist) then echo ERROR: Cannot detect low-b volumes goto error_exit endif set cmd = mri_convert set cmd = ($cmd --frame $lowblist) set cmd = ($cmd $dwidir/dwi.nii.gz) set cmd = ($cmd $dwidir/lowb.nii.gz) echo $cmd | tee -a $LF | tee -a $CF if ($RunIt) then $cmd | tee -a $LF if ($status) goto error_exit endif #= Which leads to this command: mri_convert --frame 0 14 27 41 54 68 /scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/dwi.nii.gz /scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/lowb.nii.gz And then to this error: mri_convert: extra arguments (41 and following) I made the following changes to the code (trac-preproc) and everything seems to run just fine. #= OLD set cmd = ($cmd --frame $lowblist) NEW set cmd = ($cmd --frame ${lowblist[1]}) #= What do you think? Is this just an odd-ness for me, or is it a helpful fix? One thing that I haven't been able to ascertain is whether I have an old version of mri_convert that should be able to concatenate the six listed volumes! (The next section of code seems to look like its trying to concatenate volumes so it might be expecting a 4D file? Or multiple lowb.nii.gz volumes?) I hope this all makes sense! Thank you again for all your hard work! Kx On Wed, 20 Aug 2014, Kirstie Whitaker wrote: Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!) [Note that if I've written something between then it will be specific to your files/directories etc] When running trac-all on an input nii file with corresponding bval and bvec files: 1) If you're getting an error that says: nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI NIFTI FILE Try running the command: fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE eg: fslmaths dti.nii.gz dti.nii.gz I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me. 2) If you're getting an error that says ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well. To install the update just download it (I used wget TRACULA_UPDATE_LINK) and the untar it (tar -zxvf TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory. 3) If you're getting an error that says (something along the lines of) mri_convert --frame 0 14 27 41 54 68 SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz mri_convert: extra arguments (41 and following) type mri_convert -u for usage Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http
[Freesurfer] Destrieux atlas in FSL
Hi Freesurfer and FSL communities, Firstly, I apologise for the double posting. I suspect there are experts in both groups that can help me. I'd like to be able to visualise the Destrieux atlas that freesurfer uses at the same time as my MNI standard space results in FSL. Is that possible? I'm afraid I've not been successful in my search of the mailing list archives. Thank you for your help. Kirstie -- Kirstie Whitaker, PhD Research Associate tel: +44 7583 535 307 Department of Psychiatry University of Cambridge Herchel Smith Building Robinson Way Cambridge CB2 0SZ ___ 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.