Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Re: [Freesurfer] nu_correct problem
by Gregory Kirk 18 Jan '13

18 Jan '13

Petr why do you keep trying to name your input files something.mgz, when you were in wisconsin i told you the inputs always need to be 001.mgz at this point i think you need to get invited to upload one of your data sets to ugh and see if there is a problem with the data or is it a problem with your computer. Can someone there at martinos invite Petr to upload the dataset and tell him the mechanism for doing this ? On 01/18/13, zach.petr(a)post.cz wrote: > > > > > I tried on another standar PC (4 core processor) with XP Win recon-all in VirtualBox (latest edition) running Ubuntu. > > > > I attach file folder with patient brain - first in VirtualBox as described and then in command line of terminal Ubuntu window: > > sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder > > > > Then I convert original TrioTim scanner files using mri_convert -it IMA -ot mgz filename foldername.mgz > > * here is slight problem - recon log shows that mri_convert recognizes itself that although my brain files are labeled as IMA that they are not old Siemens files, so that it unpacks them as DICOM and suggests that if it fails I should run mri_convert as DICOM > > But after all mri_convert succesfully writes foldername.mgz file as a result of conversion in foldername directory > > > > Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 > > Now -cw256 was suggested in another error run because files do not fit in 256 matrix > > Recon stops and sayz no 001.mgz files in /mri/orig directory > > So I copy converted foldername.mgz from foldername directory into /mri/orig directory and rename it to 001.mgz > > *now here is my question: do all people get 001.mgz file the same way as me? > > Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with error at nu_correct as you can see in attached recon-all.log file > > > > Petr

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pial not computing
by Borzello, Mia 18 Jan '13

18 Jan '13

Hi Freesurfers, I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m

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commands to extract thickness values
by Catherine Bois 18 Jan '13

18 Jan '13

Hi, I am trying to extract stats files from my subjects using this command aparcstats2table --hemi lh --subjects EHRS_* --skip --meas thickness --parc --aparc --tablefile lh.thick.table however I keep getting this error message Parsing the .stats files Skipping /sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/EHRS_0970_3/stats/lh.--aparc.stats Building the table.. Traceback (most recent call last): File "/usr/local2/freesurfer/bin/aparcstats2table", line 338, in ? rows, columns, table = sanitize_table(options, pretable) File "/usr/local2/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range [cbois@poplar ~]$ I have previously used this command on version 5, I now have version 5.1, have the commands possibly changed? Thanks, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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v5.2.0 beta, round two
by Nick Schmansky 18 Jan '13

18 Jan '13

For those willing and brave enough, another beta of v5.2.0 has been posted here for you to download and test: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ The Mac builds should work (note: the lion build is 64b, snow-leopard is 32b). The final release still awaits some critical improvements to the Tracula stream, but the main recon-all stream with this beta is final. The final release is expected the first week of February. Freesurfer team

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longitudinal analysis
by paul horton 18 Jan '13

18 Jan '13

Hi guys, I am currently running a longitudinal analysis on a set of scan. It is currently running and so far it has taken 5 days. It seems to be taking a large amount of time on a process called labelling slice. I have run the same analysis on other subjects which took about 6 hours to complete. So I was wondering if you know of any reason why a set of scans would take longer to process than others. I have checked the inital scans and nothing seems obviously wrong with them. Best Wishes Paul

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nu_correct problem
by zach.petr＠post.cz 18 Jan '13

18 Jan '13

I tried on another standar PC (4 core processor) with XP Win recon-all in VirtualBox (latest edition) running Ubuntu. I attach file folder with patient brain - first in VirtualBox as described and then in command line of terminal Ubuntu window: sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder Then I convert original TrioTim scanner files using mri_convert -it IMA -ot mgz filename foldername.mgz * here is slight problem - recon log shows that mri_convert recognizes itself that although my brain files are labeled as IMA that they are not old Siemens files, so that it unpacks them as DICOM and suggests that if it fails I should run mri_convert as DICOM But after all mri_convert succesfully writes foldername.mgz file as a result of conversion in foldername directory Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 Now -cw256 was suggested in another error run because files do not fit in 256 matrix Recon stops and sayz no 001.mgz files in /mri/orig directory So I copy converted foldername.mgz from foldername directory into /mri/orig directory and rename it to 001.mgz *now here is my question: do all people get 001.mgz file the same way as me? Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with error at nu_correct as you can see in attached recon-all.log file Petr

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Freesurfer vertex wise area reference
by MAHINDA YOGARAJAH 17 Jan '13

17 Jan '13

Hi, Sorry to be a little more specific - I am aware of freesurfer area references such as the WInkler reference but basically wanted a few lines, and the most appropriate references, that summarises the technical approach used for group area comparisons in qdec (using updated mris_preproc), and simple ROI group area comparisons. Thanks, Mahinda

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Merging .annot files
by Chris McNorgan 17 Jan '13

17 Jan '13

Hello all, I posted this question on the cmtk users google group, but no takers, and perhaps this is the more appropriate venue anyways. I've been successfully using cmtk within iPython. After running connectomemapper parcellate() to get the Lausanne parcellation scheme, I get six .annot files: ?h.myaparcP1_16.annot, ?h.myaparcP17_28.annot, and ?h.myaparcP29_66.annot, for each of lh and rh. Each of these .annot files label the entire cortical surface, but each of the 36 major anatomical regions (e.g., posteriorcingulate) for each hemisphere are further subdivided in only one of the three .annot files; the other two files use the original definition of the major region. In other words, in order to use these .annot files to work with the Lausanne sub-parcellations for the entire cortical surface, one has to run the same procedure using each of the 3 .annot files, and then figure out which .annot file provided the desired information. I was wondering whether it is possible to merge the three annot files to create a single .annot file for each hemisphere in which ALL of the 36 major anatomical regions have been subdivided, rather than three files containing parcellations of different subsets of these regions? Though I have been using scripts to sift through multiple sets of results to find what I'm looking for, some manual chores would be easier if I only had to work with a single file. The fact that the same vertices are labeled in all files (but are given the macro-region label in 2 files, and the sub-parcelation label in 1 file) makes me think that it's not a simple matter of concatenating the annotation files. Thanks, Chris

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problem with AutoReco3 mapping
by jonwieser＠netzero.net 17 Jan '13

17 Jan '13

I did an AutoRecon3 on a brain and when i viewed the results. it failed to classify some the tgray and white matter in the left hemisphere. the area misses is on the extreme left side of the brain, within 10 mm of the left side of the hemisphere. are there some arguments i change change to fix this. Jon Wieser jonwieser(a)netzero.com "When the going gets tough, switch to power tools." - Red Green ____________________________________________________________ One Trick to Stay Asleep If you struggle to fall asleep, or stay asleep, try this&#8230 http://thirdpartyoffers.netzero.net/TGL3241/50f85712990b57112b48st01duc

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Re: [Freesurfer] nu_correct problem (fwd)
by Louis Nicholas Vinke 17 Jan '13

17 Jan '13

Please remember to cc the list. ---------- Forwarded message ---------- Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET) From: zach.petr(a)post.cz To: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> Subject: Re: Re: [Freesurfer] nu_correct problem Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web page (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi, Documentation) I´ll send recon-all.log file later on I have it on another PC. Orig.mgz file - thats also problem. What I did: when running recon-all -subjid name -autorecon1 I get error: no /mri/orig/orig.mgz file. I looked into patients /mri directory and this path and file is not there. So that I created directory /orig in /mri and copied there converted patient.mgz file there and renamed it to orig.mgz. So that I have /subject/patient/mri/orig/orig.mgz. Maybe thats what is wrong? How do you get normally orig.mgz file? Thanks, Petr ---------- Původní zpráva ---------- Od: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> Datum: 16. 1. 2013 Předmět: Re: [Freesurfer] nu_correct problem Hi Petr, Can you provide us with some more details? Which version of FreeSurfer are you using and on what platform? Could you attach a copy of the recon-all.log file for one of these cases so we can read the full error reported? Have you tried looking at the orig.mgz which is generated prior to the mri_nu_correct.mni step to see if it looks reasonable? -Louis On Wed, 16 Jan 2013, zach.petr(a)post.cz wrote: > > > Dear members, > > when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu_correct. This happens for > DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? > > Thanks much, Petr Zach > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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