[Freesurfer] freeview bug

hi freesurfer folks, just had a nasty bug crash my whole mac workstation. yikes! i loaded lh and rh pial surfaces into freeview and went to assign annotation files to each and when i did i inadvertantly (aka randomly) selected the wrong file in labels dir- a .csv file i believe - instead of throw

Re: [Freesurfer] Running Tracula on a cluster

Hi Emily - Replace "sub238/DTI/i*.MRDC.1" with a single file name. a.y On Thu, 13 Mar 2014, ebell...@uwm.edu wrote: > Hello, > > I recently modified my script so that it would work on a cluster. I had been > running it successfully locally but am now having some trouble on the > cluster. The

Re: [Freesurfer] Running Tracula on a cluster

Hello, I recently modified my script so that it would work on a cluster. I had been running it successfully locally but am now having some trouble on the cluster. The only thing I changed in the dmrirc script were some pathways. However, I keep getting an error of must specify as many dicoms as

Re: [Freesurfer] Extracting thickness, area and folding values from Qdec

I think Doug meant the 1.3. Therefore the line should be something like: mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg What exactly did you type? (try separating it with lines instead of quotes) HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote: > Dear Doug, >

Re: [Freesurfer] Extracting thickness, area and folding values from Qdec

Dear Doug, no, I did not put it in quotes. I just typed the mentioned command, but it is still not working. I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation. Sorry for asking so many questions, but it is still not working. What

Re: [Freesurfer] Fwd: converting to fsaverage space

Hi Doug -Using the overlay threshold flags, I see that the .mgh (yes, the .mg was a cut/paste typo) is in the occipital region and should be frontal, temporal and parietal regions.  So, I must be doing something wrong in the mri_vol2surf command:> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_

Re: [Freesurfer] bvals and bvecs for dt_recon

Thxs for all the help. On March 13, 2014 at 2:19:16 PM, Louis Nicholas Vinke (vi...@nmr.mgh.harvard.edu) wrote: Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On T

Re: [Freesurfer] Fwd: converting to fsaverage space

Hi Barbara, please post to the list. Thanks! the vol2surf command output should be .mgh or .mgz, not .mg (or maybe that is just a typo in the email). If it is, then you should load the mgh file as an overlay, not as a surface, eg tksurfer [subj] lh inflated -overlay file.mgh -fminmax .5 1000

Re: [Freesurfer] bvals and bvecs for dt_recon

Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On Thu, 13 Mar 2014, Chris Watson wrote: dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (a

Re: [Freesurfer] bvals and bvecs for dt_recon

dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distr

Re: [Freesurfer] bvals and bvecs for dt_recon

The gradient table has to be in 3 columns for dt_recon. Sorry, I don't have an example because I don't use dt_recon. On Thu, 13 Mar 2014, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distrib

Re: [Freesurfer] bvals and bvecs for dt_recon

Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do you have an example? I know how to get those from private dicom tags. Gen -Original Me

Re: [Freesurfer] bvals and bvecs for dt_recon

How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format

Re: [Freesurfer] fsaverage_sym in xhemi commands

Ah! Bright! Thanks Doug! 2014-03-13 17:20 GMT+01:00 Douglas N Greve : > Just create a symlink, ie, > > cd $SUBJECTS_DIR > ln -s $FREESURFER_HOME/fsaverage_sym > > > > > On 03/13/2014 09:57 AM, Markus Gschwind wrote: > > Dear all, > > > > I have a question concerning the xhemi commands as explain

[Freesurfer] bvals and bvecs for dt_recon

Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen This email message is for the sole use of the

Re: [Freesurfer] Extracting thickness, area and folding values from Qdec

are you puttting it in quotes? If so, don't doug On 03/13/2014 01:46 PM, Dusan Hirjak wrote: > Dear Doug, > > I typed 1.3 but it is still not working. > > Any other ideas??? > > Thanks for your help. > > DH > > > Date: Thu, 13 Mar 2014 12:20:57 -0400 > > From: gr...@nmr.mgh.harvard.edu > > To: fre

Re: [Freesurfer] Fwd: converting to fsaverage space

Can you give more details? What is LECN_...nii? Where did it come from? What space is it in? MNI152 I assume? What does it mean you can't load it? Load it with what? What is your command line? doug On 03/13/2014 01:36 PM, Barbara Weiland wrote: > Hi - > > I am trying to extract volumes & th

Re: [Freesurfer] Combining scans with different scanning parameters

1 would be better but 2 would be sufficient as long as X, Y and Z don't vary too much On Thu, 13 Mar 2014, Ashley Shurick wrote: Hi Bruce (and others), We can balance the numbers to allow the same number in each configuration. But just to clarify, are you saying we should do, for example, 10 pa

Re: [Freesurfer] Combining scans with different scanning parameters

Hi Bruce (and others), We can balance the numbers to allow the same number in each configuration. But just to clarify, are you saying we should do, for example, 10 patient scan 1, 10 patient scan 2, 10 patient scan 3, and 10 HC scan 1, 10 HC scan 2, 10 HC scan 3, to perfectly balance everything ou

Re: [Freesurfer] Extracting thickness, area and folding values from Qdec

Dear Doug, I typed 1.3 but it is still not working. Any other ideas??? Thanks for your help. DH > Date: Thu, 13 Mar 2014 12:20:57 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Extracting thickness, area and folding val

Re: [Freesurfer] Fwd: converting to fsaverage space

Hi -I am trying to extract volumes & thickness stats of networks and followed the commands from the post in the subject line to create network .nii files in each subject's space.  Based on some other postings, I thought I needed to first move the volumes to surf for each hemisphere, i.e.:mri_vol2su

Re: [Freesurfer] Error mri_label2label

Hi Doug, Thank you very much! It's working! Andreia Quoting Douglas N Greve : > Not sure. Try running it with --nohash. It will probably take a lot longer > doug > > > On 03/12/2014 02:45 PM, _andre...@sapo.pt wrote: >> >> Hello list, >> >> When running the following command : >> >> mri_label2

Re: [Freesurfer] fsaverage_sym in xhemi commands

Just create a symlink, ie, cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/fsaverage_sym On 03/13/2014 09:57 AM, Markus Gschwind wrote: > Dear all, > > I have a question concerning the xhemi commands as explained here: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > 2. The command > surfreg

Re: [Freesurfer] Extracting thickness, area and folding values from Qdec

Use 1.3 not 1,3 doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: > Dear Freesurfer Experts, > > I did a correlational analysis in qdec and found several significant > clusters after Monte-Carlo simulation (0.05). > Now, I would like to extract the mean cortical thickness, area and > folding valu

[Freesurfer] 'patching' the base template with additional runs

Dear FS experts, I am trying to add a 6th and 7th timepoint to my longitudinal analysis that already has a base template from 5 timepoints. I saw an earlier response on the mailing list about doing this using a 'patch' script but there was no further information on this. Is this scrip

Re: [Freesurfer] Resting State Networks on Cortical Surface

it is in the 'vol' field On 03/12/2014 08:54 PM, Xuelong Zhao wrote: > Hmm, it seems I may have misinterpreted the fields in the matlab > structure after using MRIRead > > rsn20_surf = MRIread('rsn20_surf.nii') > > I thought perhaps the data would be in the 'volsize' field? > > rsn20_surf = > >

[Freesurfer] Longitudinal stream

Dear Freesurfer experts, I would like to perform a longitudinal analysis with freesurfer 5.1 and I have some questions regarding the whole processing stream. I have BL and 1Y follow-up from all patients (110), and moreover I have 2Y follow-up from only some patients (more or less 50). Do you re

[Freesurfer] Extracting thickness, area and folding values from Qdec

Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.

[Freesurfer] fsaverage_sym in xhemi commands

Dear all, I have a question concerning the xhemi commands as explained here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi 2. The command surfreg --s $subject --t fsaverage_sym --lh is absolutely searching for fsaverage_sym in the $SUBJECTS_DIR. Do I really have to copy the whole fsaverage