[Freesurfer] Valid options.txt file for mris_pmake (and maybe .dsh.yml too)

External Email - Use Caution Hi list! I was reading the documentation on mris_pmake (by the way, it is outdated, the documentation still asks for --surface00, at least in 7.3.2), and I would like to have a valid options.txt file to make it work with dsh (a valid example .dsh*.yml

[Freesurfer] Screenshots in Freeview within a container

External Email - Use Caution Hi! Is there any way to write freeview screenshots when running Freeview as part of a Docker container? thanks! Gari ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_mcsim OSX last version

Thanks! Don't worry, I used it in Linux. On Thu, 19 Jan 2017 at 18:40, wrote: > The new version wont work in the FS5.3 framework. Its needs to be packaged > within the development version for it to work. > > Whats the error? And does it only happen with one subject

[Freesurfer] mri_mcsim OSX last version

Hi list, mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a newer Linux version is available and indicates to ask for other versions. Is it possible to have the last osx version? thanks! Gari ___ Freesurfer mailing list

[Freesurfer] Multiple --meas files in mri_glmfit

Hi list, is it possible to have multiple --meas files in mri_glmfit? For example, for a group of 40 subjects, to check in every vertex if there is a relation between CT and the t of a fMRI contrast. Thanks! Gari ___ Freesurfer mailing list

Re: [Freesurfer] Download latest version of mris_pmake

t; > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_pmake > > > > On 11/28/2016 05:22 PM, Garikoitz Lerma-Usabiaga wrote: > > Hi, > > I am using the 2011 of mris_pmake and I've seen in the list that there > > are newer versions. > > I am using b

[Freesurfer] Download latest version of mris_pmake

Hi, I am using the 2011 of mris_pmake and I've seen in the list that there are newer versions. I am using both linux and mac. It's giving several errors when computing distances in fsaverage (just in some of the pairs), so I hope that the new version will be able to solve them. Thank you very

Re: [Freesurfer] Individual / fsaverage RAS152 discrepancies

andards). Not sure > that one is better than the other, but #2 is probably more like what is > in the liturature. > > > On 11/16/2016 04:53 PM, Garikoitz Lerma-Usabiaga wrote: > > Hi all, > > I have fMRI data in individual space, converted to individual surface > > usin

[Freesurfer] Individual / fsaverage RAS152 discrepancies

Hi all, I have fMRI data in individual space, converted to individual surface using vol2surf and to fsaverage surface using surf2surf (commands [1] and [2] below). With Matlab, I obtain the vertex with the maximum value: max_Vtx and max_Vtx305. If I would like to obtain the MNI152 coordinate of

Re: [Freesurfer] hippocampal subfields

$ freeview -Zeke On May 9, 2015, at 3:09 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi Nick! just testing it in Yosemite and gives me this error, is there any dependency I should consider? Screen Shot 2015-05-09 at 09.05.53.png On Fri, May 8, 2015 at 8:06 PM Nick Schmansky

[Freesurfer] stats from a volume ROI (in diffusion space)

Hi, I have some volume ROIs in diffusion space (1-s and 0-s). I would like to obtain, for example, the average FA values in that ROI. I tried using mri_segstats, but it gives me an error, it needs a segmentation volume. mri_segstats --i dmri/dtifit_FA.nii.gz --mask

Re: [Freesurfer] stats from a volume ROI (in diffusion space)

/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote: Hi, I have some volume ROIs in diffusion space (1-s and 0-s). I would like to obtain, for example, the average FA values in that ROI. I tried using mri_segstats, but it gives me an error, it needs a segmentation volume. mri_segstats --i dmri

Re: [Freesurfer] from label to mask diffusion space

space, the just run mri_label2vol to bring aseg into the dti space. doug On 02/02/2014 05:24 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, I've been reading the list and I ended with 4 steps to move from a label to a mask in diffusion space (below). Is this correct? Is there any other

[Freesurfer] from label to mask diffusion space

Hi Doug, I've been reading the list and I ended with 4 steps to move from a label to a mask in diffusion space (below). Is this correct? Is there any other more straightforward way? It should end with a binary mask in diffusion space (I am using the anatorig2diff.bbr.dat created in the Tracula

Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

/hippo_subfield_in_diffusion_space.nii dmri.bedpostX/merged dmri.bedpostX/nodif_brain_mask If these all come from the output of tracula, aren't these all in LAS orientation? a.y On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga wrote: Hi

Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx

dmri.bedpostX/nodif_brain_mask If these all come from the output of tracula, aren't these all in LAS orientation? a.y On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga wrote: Hi Anastasia,I want to use a hippocampal subfield as a seed in FSL. I am having problems understanding how

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Hi, sorry to jump in, but maybe this solves your problem. What I've been doing is: 1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii 2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select

Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit

Hi Rujing, About tksurfer visualization, we had the same problem, it was because the graphic card in the server, you cannot do anything about it (well, install a different one). If I remember correctly, you need a graphic card that supports OpenGL. Regards, Gari On Friday, December 20, 2013,

Re: [Freesurfer] Tracula error: libnetcdf.so.6

. Which build of freesurfer 5.3 and which build of the tracula update do you have? Using our Centos 6 build, I was not able to replicate your error. a.y On Wed, 11 Dec 2013, Garikoitz Lerma-Usabiaga wrote: Hi Anastasia, I've got this error when running -prep Tracula step. /usr/local

[Freesurfer] .nii file visualization in tkmedit

Hi list, I am trying to visualize a .nii ROI coming from MEG, which is in Colin27 space. I can visualize it perfectly in mricron and tkmedit with the following command: tkmedit -f path/to/spm8/canonical/single_subj_T1.nii -overlay MEG_ROI.nii -fthresh 0.5 (single_subj_T1.nii is Colin27) but when

Re: [Freesurfer] .nii file visualization in tkmedit

...@nmr.mgh.harvard.eduwrote: Try registering path/to/spm8/canonical/single_subj_T1.nii to Colin with bbregister doug On 12/13/2013 11:09 AM, Garikoitz Lerma-Usabiaga wrote: Hi list, I am trying to visualize a .nii ROI coming from MEG, which is in Colin27 space. I can visualize it perfectly

Re: [Freesurfer] .nii file visualization in tkmedit

...@nmr.mgh.harvard.eduwrote: Try registering path/to/spm8/canonical/single_subj_T1.nii to Colin with bbregister doug On 12/13/2013 11:09 AM, Garikoitz Lerma-Usabiaga wrote: Hi list, I am trying to visualize a .nii ROI coming from MEG, which is in Colin27 space. I can visualize it perfectly

Re: [Freesurfer] .nii file visualization in tkmedit

Mikel_SingleSubject_to_Colin.dat -om final.reg.dat Then use final.reg.dat doug On 12/13/2013 11:56 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, this is what I did. This system worked in other occasions. Could it be the problem how the volume MEG_ROI.nii was created? My colleague had a Matlab matrix

[Freesurfer] Tracula error: libnetcdf.so.6

Hi Anastasia, I've got this error when running -prep Tracula step. /usr/local/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory We have RedHat 6 (I tried in 2 different machines). Do you think it is some

[Freesurfer] Volume differences after corrections

Hi list, I obtained cortical thickness and volumetric results before and after correcting them for defects. I just did some wm edits and mostly controls points in the top of the head (some subjects had less signal so I put control points in order to allow for a good surface reconstructions).

Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6

I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com wrote:

[Freesurfer] -hippo-subfields error

Hi, I had a subject already run through recon-all. After making recon-all -s ID -hippo-subfields or recon-all -s ID -hippo-subfields -make all it is failing. It is the first subject ever failing with the hippo-subfields. The rest of the subjects are ok. This subject is properly segmented

Re: [Freesurfer] Longitudinal Freesurfer TRACULA quality control

Hi Anastasia, could explain a little bit more what do you check exactly here? What I usually look at is dlabel/diff/aparc+aseg.bbr.nii.gz, overlaid on dmri/dtifit_FA.nii.gz. Which would be the freeview command to visualize it? Thanks! Gari On Mon, Oct 14, 2013 at 11:12 PM, Anastasia Yendiki

Re: [Freesurfer] Tracula configuration error

Hi, Did you try changing the folder name? tutorial/data/dti/a226A/226A/ Maybe that's what it has to start with a letter? Just guessing. .. On Oct 13, 2013 12:02 AM, Michael Datko mikeda...@gmail.com wrote: Hello, I have been trying to set up a working Tracula configuration file and I keep

Re: [Freesurfer] Tracula bval and bvec

longitudinal fasciculus. a.y On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: Hi Anastasia, I was testing just with one subject and it finished the -prep part with error. Please find attached the trac-all.log file. As this is a test user you will see some other invocations of trac-all

Re: [Freesurfer] Red Hat 6 and Freesurfer for CentOS4/CentOS6: different results?

. The centos6 build uses a newer version of gcc which has optimization options not available on the version gcc for the centos4 build, and that makes for run-time differences in recon-all. -Zeke On 09/26/2013 08:19 AM, Garikoitz Lerma-Usabiaga wrote: Hi, I have two identical Red Hat 6 boxes

[Freesurfer] Red Hat 6 and Freesurfer for CentOS4/CentOS6: different results?

Hi, I have two identical Red Hat 6 boxes, to run recon-all-s. I just realized that in one of those I had freesurfer 5.3 for CentOS4 and in the other one I had freesurfer 5.3 for CentOS6. I have one experiment were subjects used boxes indistinctly. According to how the software is built, should

[Freesurfer] Tracula bval and bvec

Hi Anastasia, I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or

Re: [Freesurfer] TALx coordinates

Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] convert .mgh to .label?

Hi Daniel, you can use mri_surfcluster. br, Gari On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: Dear all, Is there a way to convert .mgh to .label? My .mgh is a ROI file from qdec-based group analysis and I don't want to draw the ROIs manually. Thanks!

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Hi Gari, you can use mri_annotation2label doug On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote: Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

is too trivial! Gari On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Give it the annotation (.annot) file On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote: Thanks Doug! Could you give me an example please? I cannot get it to work, with this command

[Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatically create a label from that cluster? If I use mri_binarize or mri_cor2label is not working (I

Re: [Freesurfer] Volume ROI statistics

) doug On 7/1/13 2:45 PM, Garikoitz Lerma-Usabiaga wrote: Hi, I want to obtain volume statistics from a ROI in fsaverage. I have register.dat and a .nii file (the ROI), but I don't now how to get to the .label. The last try has been: mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label

[Freesurfer] Volume ROI statistics

Hi, I want to obtain volume statistics from a ROI in fsaverage. I have register.dat and a .nii file (the ROI), but I don't now how to get to the .label. The last try has been: mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii --o $SUBJECTS_DIR/fsaverage/label/ROI.mgh --reg

[Freesurfer] REPOST: Volume ROI statistics

Hi again, is it possible to use mri_convert with a register.dat to create a .mgh volume in the registered space? any help would be appreciated... thanks! Gari On Mon, Jul 1, 2013 at 8:45 PM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi, I want to obtain volume statistics from

[Freesurfer] freeview: create ROI in inflated surface

Hi list, is it possible to create a ROI in an inflated surface within freeview or do I have to use tksurfer? It seems that I only can edit volume files. After exploratory mri_glmfit, I want to outline a ROI in fsaverage inflated surface and afterwards create a label to obtain CT averages per

[Freesurfer] Visual Word Form Area and cortical thickness

Hi list, I am interested in a Cortical Thickness analysis in the Visual Word Form Area. I have been suggested to use a MNI152 coordinate and make an sphere (circle in this case) of 5mm around it. Has anybody got any experience or any recommendation on how to establish the visual word form area

Re: [Freesurfer] Saving subjects

of control points in the WM up there should help a lot. cheers Bruce On Thu, 6 Jun 2013, Garikoitz Lerma-Usabiaga wrote: Hi list,we have some subjects with acquisition problems. Do you think it is possible to save this two subjects, and if so, how? They have been run with: recon-all -i

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

/glerma/freesurfer/subjects solved the problem. Do you think this is a problem with fs resolving sym links? We haven't found any problem with matlab or fsl. thanks again! Gari On Sat, May 11, 2013 at 12:46 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Yes, first two lines

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

with sym links, but what you have is definitely confusing! Is there any reason you have it that way? As a rule of thumb, i'd keep things as simple as possible. From: Garikoitz Lerma-Usabiaga [gariko...@gmail.com] Sent: Saturday, June 01, 2013 4:21 PM

Re: [Freesurfer] Freeview automation

=L.mgz -cam azimuth 180 Let me know if this helps. Cheers, E On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote: There is a screenshot option -ss from the command-line. Run 'freeview -h' will show you all the available options. Ruopeng On May 31, 2013, at 6:16 AM, Garikoitz Lerma

Re: [Freesurfer] Freeview automation

. Ender On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote: Thanks! I can visualize the 3D renders of interest with different colors, but from freeview -h I couldn't get the following: is it possible to automatize the File Save movie frames option? Thanks again! Gari On Fri

[Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

Hi, Has anybody got problems using FS with NFS v4? We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system. Many thanks, Gari -- Forwarded message -- From: Garikoitz Lerma-Usabiaga gariko...@gmail.com Date: Tue, May 7, 2013 at 5:25 PM Subject: NFS v4 on CentOS 5.4

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

-- Forwarded message -- From: Garikoitz Lerma-Usabiaga gariko...@gmail.com Date: Tue, May 7, 2013 at 5:25 PM Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2 To: Freesurfer freesurfer@nmr.mgh.harvard.edu Hi FS experts, we have changed our file systems to NFS v4

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

? We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system. Many thanks, Gari -- Forwarded message -- From: Garikoitz Lerma-Usabiaga gariko...@gmail.com Date: Tue, May 7, 2013 at 5:25 PM Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2 To: Freesurfer

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

? Can you output # ls -l $SUBJECTS_DIR I assume that since you say other programs can write to the filesystem, it is mounted properly, but can you show what is in /etc/fstab? i.e. make sure you see rw instead of ro. On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote: Thanks

Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

you paste the output of ls -l $SUBJECTS_DIR, so we can see what the permissions are? You may also want to paste the output of the parent directory as well. On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote: Thanks Chris, ls -l $SUBJECTS_DIR: it works This is the output of the command

[Freesurfer] NFS v4 on CentOS 5.4 or Red Hat 6.2

Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in Red Hat could not write or read. Is it a

Re: [Freesurfer] Freesurfer segmntation for ICBM or Colin27

Hi Priyanka, You can download it from the Surfrend web page and then recon-all it with the version you want (don`t use the -i, just the -s with the subject name you choose). Regards, Gari On May 7, 2013 10:56 PM, Priyanka bme.priya...@gmail.com wrote: Hello FreeSurferusers, Has anyone

Re: [Freesurfer] How to get surface-based AAL template

the Surfrend, and found there was no entry for input of register file during the processing. Looking forward to your reply. Best wishes. zhiliang At 2013-03-27 13:29:01,Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi, In my case transformation to fsaverage did not work very well. What I did

Re: [Freesurfer] How to get surface-based AAL template

Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm

Re: [Freesurfer] 3T MPRage flags

Regarding the -mprage tag, we read in the recon-all help that: -mprage : assume scan parameters are MGH MP-RAGE protocol -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. both mprage flags affect mri_normalize and mri_segment, and assumes a

Re: [Freesurfer] Correspondence of Talairach coordinates from one subject to other

of a subject to MNI305 space. You would reverse that to go from MNI305 space to another subject's RAS space thus allowing a RAS-RAS transform. If you have a surface overlay for a subject, you can use mri_surf2surf to transfer it to another subject. doug On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga

Re: [Freesurfer] Correspondence of Talairach coordinates from one subject to other

to transfer it to another subject. doug On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga wrote: Thanks Doug, I've seen the page, but I understand that everything is within the same subject. I want to find the equivalencies between subjects. I mean, the plane y = 30 in fsaverage, will correspond

Re: [Freesurfer] FS 5.2 tkmedit X11 - Xquartz Snow-Leopard

/qdec_snowleopard -Zeke Update: tkmedit 5.1 is working with Xquartz installed in Snow Leopard, tkmedit 5.2 is not working again. Any suggestion? thanks, Gari On Tue, Mar 12, 2013 at 1:16 PM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi FS experts, I just installed 5.2 for Snow

[Freesurfer] FS 5.2 tkmedit X11 - Xquartz Snow-Leopard

Hi FS experts, I just installed 5.2 for Snow Leopard in a machine who already had 5.1. When running tkmedit in 5.1 X11 works well, but when running it from 5.2 it gives the following error: BRODMANN80:~ glerma$ tkmedit bert T1.mgz dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib

Re: [Freesurfer] FS 5.2 tkmedit X11 - Xquartz Snow-Leopard

Update: tkmedit 5.1 is working with Xquartz installed in Snow Leopard, tkmedit 5.2 is not working again. Any suggestion? thanks, Gari On Tue, Mar 12, 2013 at 1:16 PM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi FS experts, I just installed 5.2 for Snow Leopard in a machine who

[Freesurfer] Correspondence of Talairach coordinates from one subject to other

Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc. Should I use vol2vol to create a volume for every subject? Is there

Re: [Freesurfer] Correspondence of Talairach coordinates from one subject to other

...@nmr.mgh.harvard.edu wrote: Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote: Hi! how can I translate a coordinate in talairach space of one subject (Colin27

Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

Hi Bruce, is there any recommended protocol for T2 acquisition to be used in the 5.2 recon-all stream? Should we used the same voxel size as the T1? (we are using 1 mm3 right now). If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just

Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

=FreeSurfer_Suggested_Morphometry_Protocols.pdf Hi Gari we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE with a FLAIR inversion pulse. Andre (ccd) can give you the details cheers Bruce On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote: Hi Bruce,is there any

Re: [Freesurfer] Hippocampus volume calculations

at 9:48 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Thanks Juan Eugenio,we have visually inspected the segmentations, and we observe that the volume differences between aseg and hippo-subfields are constants among subjects, and consistent in both left and right

[Freesurfer] Freesurfer 5.2 CentOS 4 aparcstats2table error

Hi fs experts, I have this error every time I try tu run aparcstats2table : File /home/glerma/fs/52/freesurfer/bin/aparcstats2table, line 221 with open(o.qdec, 'rb') as f: ^ SyntaxError: invalid syntax it appears each time I run aparcstats2table, even when I write:

Re: [Freesurfer] Freesurfer 5.2 CentOS 4 aparcstats2table error

Hi Nick! this is the version: Centos 4 32b or 64b (x86_64) (Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux) and the python version is: Python 2.4.3 (#1, Feb 22 2012, 16:05:45) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 (python --version

Re: [Freesurfer] Freesurfer 5.2 CentOS 4 aparcstats2table error

Thanks Nick!! is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another machine, accessing the data from a network drive? or is it a solution to run the aparcstats2table provided in 5.1 in the same machine, but accessing the data created by the 5.2 version? many thanks again for

Re: [Freesurfer] Freesurfer 5.2 CentOS 4 aparcstats2table error

$FREESURFER_HOME/bin tar xf stats2tab.tar Thanks again, Nick On Mon, 2013-02-11 at 17:06 +0100, Garikoitz Lerma-Usabiaga wrote: Thanks Nick!! is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another machine, accessing the data from a network drive? or is it a solution to run

Re: [Freesurfer] Multi-voxel pattern analysis

Hi all, is this tool going to be available to download with the 5.2? I am interested in it too. thanks! Gari On Thu, Feb 7, 2013 at 3:09 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Luisa yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm called RvoxM that I

[Freesurfer] 5.2 CENTOS x_64 ERROR tal_QC_AZS

Hi FS experts, I just downloaded the latest version again today: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0.tar.gz( 4.2 GB 1/28/13 9:47:00 PM, fsaverage has been copied to /subjects/myproject location) When running this

Re: [Freesurfer] TRACULA

Hello Anastasia and Stefano, Maybe is of little help but I wanted to let you know that I've experienced the same problem. Using exactly the same data, and using 5.1 in both cases, and having the locale set up as specified according to a solution in the mailing list: - in cent os 4 it is working -

[Freesurfer] ERROR: /52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!

Hi FS experts, I read that the current dev version for recon-all is going to be the same to the 5.2 version, so I started a new project with the dev version (in CentOS 4). I have this very strange error that I am unable to interpret, when running mpr2mni305 in one case the target is specified as

Re: [Freesurfer] AAL labels

at 7:37 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi Donald and everybody, I created AAL .mgh and .label-s in FS Colin27 space, if anybody is interested please drop me a line. best regards! Gari On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald mclaren.don

Re: [Freesurfer] AAL labels

Hi Donald and everybody, I created AAL .mgh and .label-s in FS Colin27 space, if anybody is interested please drop me a line. best regards! Gari On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald mclaren.don...@gmail.comwrote: Has anyone created an AAL label file for Freesurfer? I've done some

Re: [Freesurfer] CT Method Comparison

looking across different methods. the size of the effect is very small, about 1.5%. Do you see this as a problem? doug On 09/28/2012 05:14 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, I think that the differences are significant enough, but just in case please find attached an excel file

Re: [Freesurfer] CT Method Comparison

processing streams correctly? If so, what is the other processing stream (given in this kind of detail)? doug On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote: I have both. In origin, the ROI-s are 2mm volume based .nii that I convert to FS .mgh with register.dat I obtained with bbregister

Re: [Freesurfer] CT Method Comparison

into it and why? doug On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga (Gari) wrote: Dear Freesurfers, We've been comparing 2 different methods to obtain CT averages for 4 Volume ROI-s (volume ROI-s were in Colin27 space). We've used the 40 buckner subjects for the comparisons. METHOD

Re: [Freesurfer] CT Method Comparison

average CT intensities over them? Are the ROIs volume-based or surface-based? doug On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, many thanks for your answer, I try to detail it more: 1.- bbregister is registering two Colin27 brains. First one is a 2mm found in spm

[Freesurfer] CT Method Comparison

Dear Freesurfers, We've been comparing 2 different methods to obtain CT averages for 4 Volume ROI-s (volume ROI-s were in Colin27 space). We've used the 40 buckner subjects for the comparisons. METHOD L2L:bbregister mri_vol2surf (mgh) mri_binarize (mgh) mri_cor2label (label)

Re: [Freesurfer] mris_anatomical_stats on multiple subjects

Hi Li, there you go, Gari https://docs.google.com/open?id=0Byf71TWfovledFhJYWN2cGtHV00 On 2012-09-15, at 19:38, Kong, Li li.k...@med.uni-heidelberg.de wrote: Hi Gari, I saw your email to Alex about your method obtaining statistics from multiple subjects with Python script. Could you

Re: [Freesurfer] mris_anatomical_stats on multiple subjects

Hi Alex, I am using the same method, I created a Python script to automate it for multiple users. Basically, if you give it a file with all the subject ID-s, it maps labels with mri_label2label, obtains statistics with mris_anatomical_stats and writes all the stats in a single file. You

Re: [Freesurfer] mri_vol2surf problem

, but it will make a difference in your second call below. doug On 09/09/2012 06:13 PM, Garikoitz Lerma Usabiaga wrote: Dear freesurfers, I am trying to create .mgh labels in order to obtain CT averages from several subjects. I register the ROI-s with bbregister and I get the .nii which renders

[Freesurfer] mri_vol2surf problem

Dear freesurfers, I am trying to create .mgh labels in order to obtain CT averages from several subjects. I register the ROI-s with bbregister and I get the .nii which renders nicely in tksurfer: tksurfer Surfrend_Colin127 lh inflated -overlay

Re: [Freesurfer] mris_fix_topology stops with two T1-s

correction. Certainly it failed in this case. cheers Bruce On Fri, 10 Aug 2012, Garikoitz Lerma Usabiaga wrote: Thanks for the answer Bruce, it is still running, so I killed the process. When using two individual structural images separately, the recon-all process was OK. When I

Re: [Freesurfer] lh.ROI45.label and lh.ROI44.label overlapping

overlap. cheers Bruce On Mon, 6 Aug 2012, Garikoitz Lerma Usabiaga wrote: Hi Bruce, thanks for your answer. I am mapping a volume ROI (BA45) from SPM in MNI 152 space to fsaverage (the result is the red ROI). The problem is that: - when I load the BA45.label from FS in order

Re: [Freesurfer] lh.ROI45.label and lh.ROI44.label overlapping

by FreeSurfer, or mapping them from MNI space? In either case you can get overlap unless you pick the most probably label at each point. cheers Bruce On Mon, 6 Aug 2012, Garikoitz Lerma Usabiaga wrote: Hi freesurfers experts, this is (please check attached image) the best I got when trying

[Freesurfer] mris_fix_topology stops with two T1-s

Hi FS experts, I've run recon-all -i file -s subject -qcache -measure thickness -all to: - 18 subjects, session 1 T1 - same 18 subjects, session 2 T1 and everything went well. Then I copied the subject_id_session/mri/orig/001.mgz-s to subject_id/mri/orig/001.mgz and 002.mgz, and run the same

[Freesurfer] mni152.register.dat

Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...: tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat And I have

Re: [Freesurfer] mni152.register.dat

and 305? thanks! Gari On 2012-07-17, at 19:43, Douglas N Greve wrote: Hi Gari, Does it appear in the right place if you run tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -overlay ROI45.nii doug On 07/17/2012 01:20 PM, Garikoitz Lerma Usabiaga wrote: Hi freesurfer experts, I

[Freesurfer] Register ROI5.nii to fsaverage in tutorial Cortical Thickness of a Volume-defined ROI?

image (select: avg152T1.nii) Save it (name: ROI45.nii) 2.- I follow exactly the same steps as the tutorial, but in step 3) when I check the ROI in the inflated surface, it is clearly out of place... Thank you very much in advance, Gari Garikoitz Lerma Usabiaga Predoctoral Researcher www.bcbl.eu