Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

Also, try removing the blank line at the end of wmh.levels, and make sure you have a carriage return at the end of long.qdec.table.txt. This may fix the 2nd error On 11/09/2015 10:38 PM, Heidi Foo wrote: > Dear Dr Greve, > > Thanks for your reply. I have already linked fsaverage to my >

Re: [Freesurfer] mri_surf2surf - Interpolation

Yes, the order is preserved. On 11/10/2015 11:05 AM, Gardus III, John D wrote: > Hi Bruce and Doug, > > Thanks so much for the advice. > > I think I'll try to hack something together since I have to perform this > step for numerous subjects. > > One quick question - is the order of the vertices

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu

Are those the qdec files that generate the first error? That error implies that fsaverage is included as a subject in the qdec file. Is this possible? On 11/09/2015 10:38 PM, Heidi Foo wrote: > Dear Dr Greve, > > Thanks for your reply. I have already linked fsaverage to my > SUBJECTS_DIR but

Re: [Freesurfer] mri_surf2surf - Interpolation

Hi Bruce and Doug, Thanks so much for the advice. I think I'll try to hack something together since I have to perform this step for numerous subjects. One quick question - is the order of the vertices preserved between the pial curv and spherical curv ascii files? Thanks again, John On

[Freesurfer] mri_label2label

Hi Guys, I'm trying to map the vertices of temporal pole in one subject into the space of another subject using mri_label2label. When I do it, the output doesn't have the same number of vertices and the other of the vertex are completely messed up. See below as the first few lines in the source

Re: [Freesurfer] Region specific stats

Decide which ROIs go into each lobe, then sum or average them together. We do not have a tool do this. doug On 11/10/2015 01:28 PM, Hassan bakhshi wrote: > > Hi everyone, > > I could get all features from asegstats2table and aparcstats2table, > > Now I need stats by region, for example frontal

Re: [Freesurfer] mri_label2label

To get the same number of vertices, use --norevmap. I think it should give them to you in the same order, but I can't guarantee it. Try it on a few vertices in isolation to verify. On 11/10/2015 01:46 PM, Ray Razlighi wrote: > Hi Guys, > I'm trying to map the vertices of temporal pole in one

Re: [Freesurfer] unpacksdcmdir

Dear Douglas, Thank you! I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it? Best wishes, Baojuan From:

Re: [Freesurfer] mri_label2label

Thanks Doug, Now with —norevmap option gives 191 vertices. See below. I’m completely confused here. I have 217 vertices that I want to map them into a another subject surface. I have no problem if multiple vertices are mapping into one vertex or one vertex in source surface maps onto multiple

Re: [Freesurfer] unpacksdcmdir

Dear Douglas, Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly! Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it

Re: [Freesurfer] unpacksdcmdir

It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version On 11/10/2015 01:51 PM, Li, Baojuan wrote: > Dear Douglas, > > Thank you so much for your

Re: [Freesurfer] mri_vol2surf Matlab Function

why do you need to do it in matlab? Why not use a shell script (tcsh, sh, python, etc)? If you run it with --help, it will give you info on how to run it. On 11/10/2015 12:56 PM, Fatemeh.Molaei-Vaneghi wrote: > Dear FreeSurfers, > > I am using "mri_vol2surf" to map my SPM processed t images

Re: [Freesurfer] mri_label2label

I always wondered what is the 5th column for? Anyway seems to me it is working. I need to do more checking but this is what I did and what I got. Source Label: #!ascii label , from subject FreeSurferClean vox2ras=TkReg 5 129756 -13.048 63.016 -1.943 1 129757 -13.268 63.132 -1.961 2 129767

Re: [Freesurfer] unpacksdcmdir

Yes, seems dcmunpack does not work with our new dataset. So can I still use the images obtained from running mri_convert directly? Actually, I got the filenames for run13 by running dcmunpack and then used these filenames with mri_convert directly.

Re: [Freesurfer] unpacksdcmdir

how do you know that it is mri_convert that is causing the problem? It could be that unpacksdcmdir does not work. I've noticed that many data sets are coming off the scanner with each run in a separate folder, which breaks unpacksdcmdir. However, dcmunpack should work. On 11/10/2015 04:26 PM,

Re: [Freesurfer] applying longitudinal processing on twins

Hi Oerjan, yes, but I don't see a way to do that with the longistudinal stream. You could, however, first register surfaces across twin pairs and then go to fsaverage. You could fix cortical parcellations fixed across twin pairs on the target twin and compare ROI values across twins. You

[Freesurfer] 5.3 vs 6.0 volumetric differences...

Hi: There are any difference between subcortical structures volume, cortical thickness, supratentorial volume, gray matter volume, etc. computed with freesurfer 5.3 and 6.0 ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing

Re: [Freesurfer] mri_label2label

You can try adding a number in the statistic field (the 5th column) On 11/10/2015 02:24 PM, Razlighi, Qolamreza R. wrote: > Thanks Doug, > Now with —norevmap option gives 191 vertices. See below. > I’m completely confused here. I have 217 vertices that I want to map > them into a another subject

Re: [Freesurfer] mri_label2label

looks like it works. I don't think not hashing will have an effect (except to slow it down) On 11/10/2015 02:49 PM, Razlighi, Qolamreza R. wrote: > I always wondered what is the 5th column for? > Anyway seems to me it is working. I need to do more checking but this > is what I did and what I

Re: [Freesurfer] unpacksdcmdir

yes On 11/10/2015 04:35 PM, Li, Baojuan wrote: > Yes, seems dcmunpack does not work with our new dataset. > So can I still use the images obtained from running mri_convert directly? > Actually, I got the filenames for run13 by running dcmunpack and then used > these filenames with mri_convert

Re: [Freesurfer] unpacksdcmdir

Use the development environment (but only for unpacking) source /usr/local/freesurfer/nmr-dev-env On 11/10/2015 02:31 PM, Li, Baojuan wrote: > Dear Douglas, > > Thank you! > > I am using a desktop of the Martinos Center. Seems I am not allowed to > replace the mri_convert file under the

Re: [Freesurfer] mri_surf2surf - Interpolation

as long as it is the same subject/hemi, then yes On Tue, 10 Nov 2015, Gardus III, John D wrote: > Hi Bruce and Doug, > > Thanks so much for the advice. > > I think I'll try to hack something together since I have to perform this > step for numerous subjects. > > One quick question - is the order

Re: [Freesurfer] mri_label2label

Great, Thank you so much. -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razli...@gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website:

Re: [Freesurfer] unpacksdcmdir

Dear Douglas, This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error: The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI

Re: [Freesurfer] unpacksdcmdir

Good news! Thank you :) 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: Tuesday, November 10, 2015 4:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

Re: [Freesurfer] mri_vol2surf Matlab Function

Are you saying that you have the actual surface data stored as an array in matlab or just the filename pointing to the surface data. The routine that you have there will not work because mri_vol2surf is a linux command. However, you can run linux commaand from matlab using the matlab "system"

Re: [Freesurfer] 5.3 vs 6.0 volumetric differences...

Hi Gonzalo, of course. There is even a difference when running the same FS version with a different operating system (due to differences in the numerical libraries, optimizations etc). Are changes big or small? In a single case they can be very big (it could be a case that failed in 5.3 and

[Freesurfer] Error viewing uncorrected sign map with freeview

Dear Freesurfer group - I am receiving the following error when I try view results of a mri_glmfit. Any assistance would be greatly appreciated. Thanks, Chaz freeview -f

Re: [Freesurfer] Error viewing uncorrected sign map with freeview

are you using 5.3? I think that option is only supported in version 6. Try removing :annot_outline=1 On 11/10/2015 05:43 PM, Gay,Charles Wysaw wrote: > Dear Freesurfer group - > > I am receiving the following error when I try view results of a > mri_glmfit. Any assistance would be greatly

Re: [Freesurfer] mri_vol2surf Matlab Function

Dear Douglas, Thanks for your reply. The reason I want to use mri_vol2surf in Matlab is that I have a huge dataset saved in cell arrays of Matlab i.e. multiple subjects, multiple datasets for each subject, multiple ROIs for each of these datasets, multiple surfaces for each of these ROIs, and

Re: [Freesurfer] registration format conversion

Alright, got it working! Thanks! Any chance I can also get the mri_concatenate_lta mentioned here? http://ftp.nmr.mgh.harvard.edu/pub/docs/wiki/lta_convert.help.xml.html stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA //

Re: [Freesurfer] registration format conversion

here you go ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_concatenate_lta On 11/10/2015 07:13 PM, S.V.Shepherd [work] wrote: > Alright, got it working! Thanks! > > Any chance I can also get the

Re: [Freesurfer] applying longitudinal processing on twins

Thank you for the quick reply! I've been elaborating with a ROI-based approach for VBM where I first create an unbiased template for each MZ-pair (non-linear registration; ANTS SyN); second, create a group template in MNI-space where ROIs are defined; third, warp each pair template to the group

[Freesurfer] Tracula bedpostx terminated

Dear Freesurfer experts, I am running tracula v5.3.0 on OpenSuse. I successfully ra ​​ n freesurfer ​ ​ reconstruction ​ ​ and trac-all-prep. However, when I try to run trac-all -bedp -c ​ ​ dmrirc_file, I get the following ​message: ​​ 47 s​ lices processed 48 ​ s​ lices processed ​50​ s​

Re: [Freesurfer] registration format conversion

try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_concatenate_lta On 11/10/2015 07:31 PM, S.V.Shepherd [work] wrote: > I think that one got garbled slightly. Can you try again? > > _stephen v. shepherd phd_ > The Rockefeller University / 1230 York Avenue / New

Re: [Freesurfer] registration format conversion

I think that one got garbled slightly. Can you try again? *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699 On Tue, Nov 10, 2015 at 7:29 PM, Douglas N Greve wrote: > here you go > >

Re: [Freesurfer] mri_surfcluster statistics and label question

Thanks! The F.mgh works well, and it also increases precision as converting from the exponent itself is less precise. -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/9/15, 10:57 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve"