[Freesurfer] mris_preproc patch

Dear Doug, I would need the mris_preproc patch, however the link provided (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc) is not working. Is there another way of getting the patch (rather than downloading the new version of FreeSurfer)? Best wishes, Nenad ***

[Freesurfer] Pial surface area

Hi mailinglist, I want to obtain aparc.stats for pial instead of white matter surface area. I read that I therefore should adjust mris_anatomical_stats. However, when I run this command separately, the following error occurs: cannot allocate memory Then I tried to put autorecon3 -parcstats in fr

Re: [Freesurfer] Pial surface area

Hi Anita you need to include the full command line and screen output for us to help you. cheers Bruce On Fri, 21 Mar 2014, Anita van Loenhoud wrote: Hi mailinglist, I want to obtain aparc.stats for pial instead of white matter surface area. I read that I therefore should adjust mris_anatomic

Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

Dear Doug, I'm very thankful for your helpful comments! I will check the feat2surf script and apply it to map FSL-data in individual and common space (preconditions: existing FEATdir with non-smoothed EPI's and applied reg-feat2anat). I will make use of the -projfrac 0.5 to sample in the middle

Re: [Freesurfer] mri_convert .tar.gz files of dicoms?

Huh, will you look at that: $ time find s04_epi -type f |sed 1q s04_epi/s04_epi.0001 real 0m0.096s user 0m0.002s sys 0m0.014s $ time tar tf s04_epi.tar.gz |sed 1q s04_epi/s04_epi.0001 real 0m0.016s user 0m0.001s sys 0m0.008s Thanks! (Also, modern 'tar' seems to figure out compression on its ow

Re: [Freesurfer] Pial surface area

Hi Bruce, See below. Thank you! Anita First I tried: *aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$ *mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial INFO: assuming MGZ format for volumes. co

Re: [Freesurfer] Pial surface area

Hi Anita mris_anatomical_stats isn't a flag to recon-all. It is it's own binary that you should call directly from the command line. For the znzTAGskip error, this was a bug we briefly had but hasn't been around in a long time. Can you try downloading a new version? What version did you use t

Re: [Freesurfer] reconstruction problem with pediatric images

Hi Francesco, Given that the recon pipeline is built on an adult atlas it is not expected to work for such young subjects. In the past, with high quality images, we managed to get reasonable recons for ages down to 4 (or sometimes 3). For the younger population though it will not work. We are

Re: [Freesurfer] mri_convert .tar.gz files of dicoms?

On Thu, Mar 20, 2014 at 5:58 PM, Chris Watson wrote: > FYI, you can also get the first file like this: > > first_file=$(tar ztf ${in_file} | head -1) Not to beat this to death, but sometimes this returns a directory name instead of a file name. So `find -type f` is safer, unless there's some way

Re: [Freesurfer] Pial surface area

Hi Bruce, The wm.mgz was created a while ago with an older version, by another student. At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent version, or is there another option? Thank you, Anita ___ Freesurfer mailing list Freesu

Re: [Freesurfer] Anonymizing Siemens DICOM files

Thanks to all that have replied so far! Bruce, are you referring to this: http://freesurfer.net/fswiki/BIRND-UP ? Thanks, Caspar 2014-03-20 17:40 GMT-04:00 Harms, Michael : > > Hi Caspar, > I can't address your question regarding a specific tool, but wanted to > mention a note of caution. > Yo

Re: [Freesurfer] mris_preproc patch

you can get it from this page. You don't need the other files unless you are doing the interhemispheric analysis http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 03/21/2014 04:41 AM, N. Medic wrote: > Dear Doug, > > > I would need the mris_preproc patch, however the link provided > (ftp://surfer

Re: [Freesurfer] Pial surface area

yes, try that and see if it resolves the problem On Fri, 21 Mar 2014, Anita van Loenhoud wrote: > Hi Bruce, > The wm.mgz was created a while ago with an older version, by another > student. > > At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent > version, or is there anot

Re: [Freesurfer] localgi make_outer_surface

Hi Charnjit, that script is Maria's code I think (which is why it is a good idea to post to the list and not to us personally :-) doug On 03/21/2014 07:28 AM, Charnjit Sidhu wrote: > Hi Doug, > > I think the problem is similar to the following post on the mailing lists: > > https://www.mail-arch

Re: [Freesurfer] Converting volume from fsaverage to subject space

When you say the MNI305 space, do you mean the 2mm space that is the output of FSFAST? If so, then first run reg-mni305.2mm to create the appropriate registration file. Then use this registration file when running mri_vol2vol doug On 03/20/2014 02:39 PM, Omar Singleton wrote: > Hello Freesurf

Re: [Freesurfer] Anonymizing Siemens DICOM files

yup, that's it thanks Caspar Bruce On Fri, 21 Mar 2014, Caspar M. Schwiedrzik wrote: Thanks to all that have replied so far! Bruce, are you referring to this: http://freesurfer.net/fswiki/BIRND-UP ? Thanks, Caspar 2014-03-20 17:40 GMT-04:00 Harms, Michael : Hi Caspar, I can't address your qu

Re: [Freesurfer] tkmedit contrast

Is it just when you use the MIP or whenever you view it? Are the values between 0 and 255? doug On 03/20/2014 01:28 PM, Borzello, Mia wrote: > picking the electrode points for an intracranial patient. I can usually do it > pretty easily in tkmedit, but I'm just getting an odd contrast with this

Re: [Freesurfer] localgi make_outer_surface

Ok sorry, new to this mailing lark, will post to mailing list :-) Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 21 March 2014 15:56 To: Cha

Re: [Freesurfer] Flipping left-right hemispheres

I tried your suggestion (using subjTP/xhemi in place of subjTP) in the qdec table. I doesn't work because long_mris_slopes uses subjTP and subjBase to create "subjTP.long.subjBase", the directory of the actual data. Extra slashes "/" in the name create an incorrect name (i.e. subjTP/xhemi.long.subj

Re: [Freesurfer] Flipping left-right hemispheres

mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg Martin, can you modify long_mris_slopes to add this? But another question is exactly what you want to do in the end. What function of the slopes and hemisphere are you trying to compute? doug On 03/21/2014 01:20 PM, P

Re: [Freesurfer] Segmentation fault:11 with mris_anatomical_stats {Disarmed}

Thank you Doug. I was using the same label file for all subjects before. I will create the labels for each individual and run the mris_anatomical_stats ( I tested it on one subject that didnt run before, and it did not give any errors this time) Thanks again! Rupa It looks like this label w

Re: [Freesurfer] Calculating Total White Matter

Thank you for your response. But just to clarify a bit further, in the asegstats2table there are values given for TotalGrayVol. I am assuming this includes both subcortical and cortical measures for GM along with cerebellar values, etc. Likewise, I am looking for TotalWhiteVol or a way of calcul

Re: [Freesurfer] Anonymizing Siemens DICOM files

You could also do it the following way: (you need to download dcmtk) Assuming you have a bunch of files called MR.* for dicom in MR.* do dcmodify -m "(0010,0010)=PatientsName" ${dicom} dcmodify -m "(0010,0030)=MMDD" ${dicom} done This backs up all the dicoms (they become "MR.*.bak"),

Re: [Freesurfer] Calculating Total White Matter

Hi Elizabeth, The measure called "CorticalWhiteMatterVol" *is* the total cerebral white matter. See this page: http://freesurfer.net/fswiki/MorphometryStats The values for the "{lh,rh}CorticalWhiteMatterVol"measures in aseg.stats used to be the same as that returned by the 'mris_wm_volume' functi

Re: [Freesurfer] Flipping left-right hemispheres

The overall question is: did the cortical thickness of healthy hemispheres (of stroke subjects) change from tp1 to tp2, and does it correlate with the change in their functional measure? So I was using the long.thickness-rate measure and qdec. Peggy On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Gre

Re: [Freesurfer] Flipping left-right hemispheres

Is the time between tp1 and tp2 the same for all subjects? If not, are you using that information? On 03/21/2014 04:15 PM, Peggy Skelly wrote: > The overall question is: did the cortical thickness of healthy > hemispheres (of stroke subjects) change from tp1 to tp2, and does it > correlate wit

[Freesurfer] use 1 vs. 2 T1 acquisitions

Hello freesurfer gurus, We acquire 2 BRAVO T1s on a GE 3T during the same scan session on most of our study participants, but because of various issues, occasionally only get 1 T1/participant. I've been processing the data combining both T1s when we have 2 and using just 1 T1 when that was all

Re: [Freesurfer] Flipping left-right hemispheres

The actual time between tp1 & tp2 varies for subjects, *but* every subject received the same "dose" of treatment between timepoints. To ask if the treatment changed a subject's cortical thickness, I'm not using the actual time difference, I'm using a constant 1 for the time difference. (i.e. in lon