Re: [Freesurfer] Found 0 unique series

You don't need a .dat file, it just could not create the file. It was trying to create it in /autofs/cluster/cagn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/ do you have write permissions into that folder? On 6/15/16 5:01 PM, Raney, Talia L. wrote: > This is true, but in other

[Freesurfer] wm.mgz edits

Dear all, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity

Re: [Freesurfer] convert from MNI152 to native space

Hi Doug, Thanks for your reply. When I run mni152reg I get an error : ERROR: Flag --lta unrecognized I'm using v 1.9 of this file. I found a post that said to download a newer version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg but it doesn't seem to be

Re: [Freesurfer] registering to fsaverage

worked beautifully. Thank you! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve wrote: > Try surf2surf with --mapmethod nnf > > On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote: > >

Re: [Freesurfer] Found 0 unique series

This is true, but in other subjects, I never had to create a .dat file while running dcmunpack. It's saying there is no .dat file in the output directory not the input directory. When I run debug, I get this: set filetype = `mri_probedicom --i $f --d filetype` set filetype = `mri_probedicom --i

Re: [Freesurfer] selxavg3-sess error

Thank you, I'll try! Best Francesca On Wednesday, June 15, 2016, Douglas N Greve wrote: > Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST > needs both. If you don't have polar, just copy the eccen data and call > it polar. for what you want

Re: [Freesurfer] Fwd: Getting the pial surface to cover the entire medial temporal lobe structures

I would try Bruce's idea first, but another option would be to run mri_tesselate on the aseg volume you had loaded in those images. hth d On Wed, Jun 15, 2016 at 4:46 PM, Bruce Fischl wrote: > Hi David > > we don't have anything that does this by default, sorry. If

Re: [Freesurfer] Fwd: Getting the pial surface to cover the entire medial temporal lobe structures

Hi David we don't have anything that does this by default, sorry. If you don't care about the location of the white surface you could try setting all the voxels in the wm.mgz that are left or right hippo/amygdala in the aseg to 255 then running from autorecon2-wm forward. cheers Bruce On

Re: [Freesurfer] Found 0 unique series

The problem appears to be cat: /imagelist.dat: No such file or directory Not sure what is going on there. Make sure you're not in / when running it or that the output points to /. Try running it with -debug as the first argument and sending the output. On 06/15/2016 04:36 PM, Raney, Talia L.

Re: [Freesurfer] registering to fsaverage

Try surf2surf with --mapmethod nnf On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote: > Hi Doug - yes they do actually, I was quite pleased. I did some trials > with other subjects and the mri_vol2surf all looks good. Very similar > to what I had in our in-house software. > > Would things be

Re: [Freesurfer] Found 0 unique series

My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run $run_num restingstate nii.gz f.nii.gz and the output is --- 1 24 restingstate f 0 0 --- Searching for matching files Wed Jun 15 16:34:27 EDT 2016

Re: [Freesurfer] registering to fsaverage

Hi Doug - yes they do actually, I was quite pleased. I did some trials with other subjects and the mri_vol2surf all looks good. Very similar to what I had in our in-house software. Would things be better if I were to isolate each sulcus as a .label and then try the mri_label2label? Someone

Re: [Freesurfer] registering to fsaverage

The problem is probably that the vol2surf command did not properly sample the labels onto the surface. Do the labels on subject 00350 surfaces look ok? On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote: > thanks Dr. Fischl > > So the command seems to have worked! I have copied what ran in my

Re: [Freesurfer] Found 0 unique series

what is your command line and what is the full terminal output On 06/15/2016 04:06 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I've been running dcmunpack and I get an error that said Found 0 unique > series, even though it has dicom files. What does this mean and what could I > do to

Re: [Freesurfer] Maps/seed on surafce

what was your mkanalysis-sess command? On 06/08/2016 02:10 PM, Martin Juneja wrote: > Dear FreeSurfer and SPM experts, > > I am trying to calculate functional connectivity maps using FreeSurfer > pipeline: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough. > >

[Freesurfer] Found 0 unique series

Hi FreeSurfer users, I've been running dcmunpack and I get an error that said Found 0 unique series, even though it has dicom files. What does this mean and what could I do to fix the problem? Best, Talia ___ Freesurfer mailing list

Re: [Freesurfer] selxavg3-sess error

Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST needs both. If you don't have polar, just copy the eccen data and call it polar. for what you want to do it won't make much difference. On 06/08/2016 09:55 AM, Francesca Strappini wrote: > I have only something similar in

[Freesurfer] Final Call for Papers SAN2016

Dear colleagues, please, accept our advanced apologies for any multiple cross-postings... The Society of Applied Neuroscience (SAN, http://www.applied-neuroscience.org/) in cooperation with the Medical School of the Aristotle University of Thessaloniki and the Department of Neurology of the Max

[Freesurfer] unit for hippocampus segmentation results

Hi freesurfer experts, We used the development version of freesurfer 6.0 to segment hippocampus. We are wondering what the unit is for the segmentation results. Thanks, -- Fengji Geng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Convert ascii to .mgh

Dear Doug Thank you for your answer. I however encounter an error: >> F.vol = fast_mat2vol(lfdr,F.volsize) ERROR: szvol inconsistent with mat2d I have attached the final output (.mgh) and the .asc file. (As the files are too large, I added them here: https://we.tl/MKhhmeT5Zn) Thank you Robby

Re: [Freesurfer] SIENAX

maybe you want to check with the FSL group? It really depends on what measures you want to obtain On Wed, 15 Jun 2016, Hassan bakhshi wrote: > We have some cases which we want to process , I searched about SIENAX and as > you are more expert in this area, I wanted to know > Freesurfer

Re: [Freesurfer] SIENAX

We have some cases which we want to process , I searched about SIENAX and as you are more expert in this area, I wanted to know Freesurfer preferences on SIENAX ??? The other thing is process time in these two software. Kind Regards, ___ Freesurfer

[Freesurfer] Memory

Is there any way to check how many autorecon processes I can run at the same time? I am using a linux with 16gb ram. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] -hippocampal-subfields-T1T2

Hi All, Was this issue solved?? I am getting the similar error but couldn't find a solution on the mailing list. Fitting mesh to synthetic image from ASEG took 362.0884 seconds Transforming points Transforming points set final LTA type to 1

Re: [Freesurfer] registering to fsaverage

Hi Trisanna you would only use those options of if you were transforming a surface Bruce On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: thanks Dr. Fischl I assume that for surface overlays one cannot specify --sval-xyz and --tval-xyz or the command will treat the input as a surface

Re: [Freesurfer] registering to fsaverage

thanks Dr. Fischl I assume that for surface overlays one cannot specify --sval-xyz and --tval-xyz or the command will treat the input as a surface itself? best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 15, 2016 at 11:11 AM,

Re: [Freesurfer] convert from MNI152 to native space

You'll need a registration that goes from the functional to the mni152. This has to be done in two steps, 1. Run mni152reg --s subject to create the anat-to-mni152 registration (needs FSL) 2. Run bbregister to get the anat-to-func reg (in lta format) 3. then combine them with

Re: [Freesurfer] Convert ascii to .mgh

I would do it in matlab, eg, F = MRIread('F.mgh'); % This is to get the proper header information lfdr = load('lfdr.asc'); F.vol = fast_mat2vol(lfdr,F.volsize); MRIwrite(F,'lfdr.mgh'); On 6/15/16 4:45 AM, Robby De Pauw wrote: Dear FreeSurfer users, To address the problem of multiple

Re: [Freesurfer] Coregister the CT image and MRI image

use mri_vol2vol, like mri_vol2vol --mov CT.nii --reg v1t2.lta --fstarg --o CT-in-anat.nii On 6/15/16 9:58 AM, HARI GURAGAIN wrote: Dear Douglas, With the suggestions from Zeke, the mri_coreg is working now. I have one last question: I got the new v1to2.lta. How to apply this transformation

Re: [Freesurfer] Define the design matrix by myself

The 1st and 2nd column add up to the 3rd and 4th column. To do this type of model, you'll have to have 1. A column of 1s (like you had before) 2. Get rid of columns 2 and 5. This makes the 1st column of all 1s represent a CN-female. the (new) 2nd column is the additive effect of AD. You'll

Re: [Freesurfer] registering to fsaverage

Hi Trisanna you don't need to inflate the overlays. They can just use the existing surface-based (sphere.reg) registration. cheers Bruce On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: Hi there So I have sulcal labels from another software (.mnc format) from which I am trying to

[Freesurfer] registering to fsaverage

Hi there So I have sulcal labels from another software (.mnc format) from which I am trying to generate some probability maps. I was able to convert the .mnc to .mgz surface overlay using mri_vol2surf for my MRIs after running all MRIs in recon-all. So, now I have all my painted voxels as surface

Re: [Freesurfer] Fwd: concerting surface format

Look at mris_convert. If that doesn¹t help would also see if BrainVisa allows conversion to a third format that mris_convert works with. Finally, does BrainVisa not support GIFTI (the standard, cross-neuroimaging software surface format)? Peace, Matt. From:

Re: [Freesurfer] Fwd: concerting surface format

Hello Trisanna, as pointed out by Matt as I started to write this email, the solution is in the Gifti format. If you install brainvisa, it provides tools to convert from .mesh to .gii. You can then read these in FreeSurfer or convert them using mri_convert. You can write to me privately if you

Re: [Freesurfer] Fwd: concerting surface format

Hi Trisanna, perhaps check with the BrainVisa people? We don't know the specs of that format. Maybe you could read it into matlab, then write it out in our format with write_surf.m? cheers Bruce On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: > > > Hi there > > is there a way to convert

[Freesurfer] Fwd: concerting surface format

Hi there is there a way to convert .mesh (BrainVisa) to the Freesurfer surface format? mri_convert doesn't seem to do it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

Re: [Freesurfer] Compile and Install on El Capitan

Ill be attempting a build on an El Capitan machine today and will update the page accordingly. -Zeke On 06/15/2016 04:48 AM, Aziz Nanthaamornphong wrote: > Hi, > > Can we compile & install Freesurfer on El Capitan? Unfortunately, I > found the document for Lion >

Re: [Freesurfer] Coregister the CT image and MRI image

Dear Douglas, With the suggestions from Zeke, the mri_coreg is working now. I have one last question: I got the new v1to2.lta. How to apply this transformation to the CT image? Is it by using mri_convert? Something like below? mri_convert -at v1to2.lta CT.nii new_CT.nii Any suggestion will be

Re: [Freesurfer] Define the design matrix by myself

Glad to know the fsgd file explanation:) I have deleted the first colum(constant column, I made a simple mistake), but it didnt work even without the constant column, I got the same error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07

Re: [Freesurfer] SIENAX

Hmmm, I'm not sure I understand your question. SIENAX is indeed from the FSL group and different than what we do. What are you trying to accomplish? On Wed, 15 Jun 2016, Hassan bakhshi wrote: Hi, I lately heard about SIENAX and when I looked into it it seems like Freesurfer,  using the

[Freesurfer] controlling for ICV in LME

Dear FreeSurfer experts, I conducted a study with 3 groups of children (2 trainings, 1 control) and I want to analyze them longitudinally with LMEs. While preparing my data 2 topics came up that I would like to know more about. A. controlling for ICV/mean thickness/surface area 1) I want to

[Freesurfer] convert from MNI152 to native space

Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in

[Freesurfer] SIENAX

Hi, I lately heard about SIENAX and when I looked into it it seems like Freesurfer, using the same brain extraction process and etc. I wanted to ask if it is more complete than Freesurfer or not? and why researcher are going after it? It is for Oxford University I think. Kind Regards,

[Freesurfer] Compile and Install on El Capitan

Hi, Can we compile & install Freesurfer on El Capitan? Unfortunately, I found the document for Lion ( https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page). Thank you, Aziz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Convert ascii to .mgh

Dear FreeSurfer users, To address the problem of multiple comparison, I wanted to apply the localfdr-method. For this purpose, I need the F-statistic (which I can extract from the F.mgh scalar overlay I presume?). I converted this to an ascii-file, which I was able to load into R, using the

Re: [Freesurfer] tkmedit

Thanks! I will use it. Best,  Kojima  - Original Message - >From: Bruce Fischl >To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list > >Date: 2016/6/15, Wed 10:32 >Subject: Re: [Freesurfer] tkmedit > >yes! >On Wed,