Re: [Freesurfer] identity.nofile

Can you load another label, eg, lh.cortex.label? Also, I noticed that there is a space between "label=" and "/data/..." in the command line below. That space should not be there, so if it was there when you ran the command try again without the space. On 4/19/16 9:19 PM, Trisanna Sprung-Much

Re: [Freesurfer] identity.nofile

Hi Trisanna your output is a .mgz file, which is *not* a label. Try loading it as an overlay. The label format is different (ascii for one thing, and only part of the surface for another). cheers Bruce On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: Hi Doug I thought this was the case

Re: [Freesurfer] identity.nofile

Hi Doug I tried again in the terminal and got this: *trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * [0]PETSC ERROR:

Re: [Freesurfer] identity.nofile

Hi Doug I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal: trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x29080920 *** Abort (core

[Freesurfer] Convert retenotopic areas from brainvoyger to Freesurfer

Hello I intend to compute cortical thickness in retinotopic areas. However retinotopic areas were delimited in BrainVoyager and the cortical thickness maps with FreeSurfer. There are any way to reconcile data from the two softawares? -- Com os melhores cumprimentos, Lília Jorge

Re: [Freesurfer] identity.nofile

I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path On 04/19/2016 05:45 PM, Bruce Fischl wrote: > Hi Trisanna > > if your output is .mgz it isn't a label file. Labels are stored in > .label names and are text files. The .mgz is a scalar

Re: [Freesurfer] identity.nofile

Hi Trisanna if your output is .mgz it isn't a label file. Labels are stored in .label names and are text files. The .mgz is a scalar field over the surface (that is, a vector with a single value at each surface location). In freeview you can view it as: freeview -f

Re: [Freesurfer] identity.nofile

Hi Doug So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. *However, when I then try to open the pial surface and the corresponding new label in freeview, it says it

Re: [Freesurfer] white matter edits not incorporated

Hi Bruce, Thanks! I'll give it a whirl. d On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl wrote: > Hi Daniel > > the problems isn't that it it's ignoring the wm edits, it is that it starts > the orig surface out there, but then retracts to the (same) visible >

Re: [Freesurfer] white matter edits not incorporated

Hi Daniel the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the

Re: [Freesurfer] white matter edits not incorporated

can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote: > Just to follow up, I have tried several different options with > recon-all to get the white matter edits to stick on this participant, > and it doesn't seem to be

Re: [Freesurfer] white matter edits not incorporated

Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working: re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all I can't seem to get any

Re: [Freesurfer] identity.nofile

many thanks - will give this a go! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve wrote: > yes, but the surface overlay is in mgz (or nii.gz) format > > On 04/19/2016 03:05 PM,

Re: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr

That means that there are no voxels in the final ROI in native functional space. You should check your registration and also see how big your original ROI is. On 04/15/2016 11:32 PM, Julio Alberto González Torre wrote: > I performed the preprocessing again with -per-run parameter. > Everything

Re: [Freesurfer] Segmentation Fault during mri_glmfit-sim

There is nothing obvious going wrong. If the exact same command sometimes fails and sometimes works, then it may be a problem on your system. In any event, without a reproducible error, I can't really debug it. On 04/15/2016 08:31 PM, Elijah Mak wrote: > > On another note, I am running into a

Re: [Freesurfer] PET voxelwise

On 04/15/2016 08:31 PM, Elijah Mak wrote: > No, more like running the voxelwise comparisons only on voxels that > have positive BP between 2 group. Is that possible? I'm still not sure what you mean by "positive BP between 2 group". Do you mean masking out voxels where either group is less

Re: [Freesurfer] mkanalysis-sess stimulusdelay parameter

That was set assuming that the data have been slice-time corrected to the middle of the TR. On 04/19/2016 02:31 PM, Joseph Dien wrote: > I’m taking a look at the effects of stimulus delay settings in one of > my datasets so I was surprised to notice that the default setting > of

Re: [Freesurfer] identity.nofile

yes, but the surface overlay is in mgz (or nii.gz) format On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and

Re: [Freesurfer] identity.nofile

sorry for the confusion. Some of our tools use identity.nofile, but these use --regheader cheers Bruce On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: Hi Doug below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the

Re: [Freesurfer] identity.nofile

Hi Doug below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the transformation since my labels and T1s are already in the same space and I just want to resample my labels to the surfaces. *I will try, as you suggest,

Re: [Freesurfer] CA2 hippocampal subfield in FS6.0

Yes! Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Patrick Sezen" To: "Freesurfer support list"

[Freesurfer] mkanalysis-sess stimulusdelay parameter

I’m taking a look at the effects of stimulus delay settings in one of my datasets so I was surprised to notice that the default setting of mkanalysis-sess is a delay of -TR/2 seconds. What is the reasoning for this? If, as I expect, it was just empirically found that it worked better than

Re: [Freesurfer] identity.nofile

I'm not sure what identity.nofile is or what you are trying to do (no previous info in the email). If whatever you are trying to map to the surface is already in anatomical space (so no registration necessary), then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

are you sure the label file is really a label file? Does the same thing happen if you specify -l labelfile on the command line? On 04/18/2016 05:08 PM, DeCross, Stephanie N. wrote: > I can open the nii.gz output of the first step (vol2vol) just fine. But the > .label output of the second step

[Freesurfer] identity.nofile

Hi All! Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

Can you run /mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/ |& tee dng.log and send me dng.log ? doug On 04/18/2016 04:51 PM, Mcnorgan, Christopher wrote: > du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is > the “not found” error telling me that a binary is not found,

Re: [Freesurfer] entorhinal & temporal pole thickness measurements

Hi Mihaela adolescent girls probably have thicker cortex than older kids/adults. One thing to watch our for is dura/tentorium. Particularly when the cortex is thick it can be adjacent to cortical gray matter and difficult/impossible to avoid including in the cortical ribbon unless you have

[Freesurfer] entorhinal & temporal pole thickness measurements

Dear Freesurfers, We noticed that some subjects in our study have the average cortical thickness values in entorhinal and temporal pole above 4 mm. They are adolescent girls so they're pretty young but we wonder if these values are accurate. Visually, their segmentations seem good. In an older

Re: [Freesurfer] temporal lobe pial surface problem

OK. I will do it. Xiaomin Date: Tue, 19 Apr 2016 10:56:15 -0400 From: fis...@nmr.mgh.harvard.edu To: yu...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem then you need to put some control points in the white

Re: [Freesurfer] Preprocessing task data with multiple B0-corrected runs

One of the tasks we use has three runs, and so each run has a specific B0 map. We're wondering how we can concatenate the three runs back together again for the Group analysis, since FSFAST is technically now considering each run to be a separate "task." -Original Message- From:

Re: [Freesurfer] temporal lobe pial surface problem

then you need to put some control points in the white matter. 70 is way too low On Tue, 19 Apr 2016, Xiaomin Yue wrote: The white matter in the anterior temporal lobe is around 70, the gray matter is about 30.  The number is read from brain.finalsurfs.mgz. Xiaomin > Date: Tue, 19 Apr 2016

Re: [Freesurfer] temporal lobe pial surface problem

The white matter in the anterior temporal lobe is around 70, the gray matter is about 30. The number is read from brain.finalsurfs.mgz. Xiaomin > Date: Tue, 19 Apr 2016 09:29:50 -0400 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > CC: macar...@libero.it;

Re: [Freesurfer] temporal lobe pial surface problem

Hi Bruce, the data was uploaded to the ftp site. The file name is xyueSubj.mgz. thanks,Xiaomin From: fis...@nmr.mgh.harvard.edu Date: Mon, 18 Apr 2016 22:58:30 -0400 To: freesurfer@nmr.mgh.harvard.edu CC: macar...@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem It's

[Freesurfer] how to add skull and scalp and how to convert RAS coordinates

Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues: 1. How can I add the CSF, the skull and the scalp in my model?

Re: [Freesurfer] Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04

Hi Nasos tkmedit has been deprecated for a few years. Can you try freeview? cheers Bruce On Tue, 19 Apr 2016, Nasos Petridis wrote: > Hello, > > Recently, I started using freesurfer on a Ubuntu system. I've noticed > two issues, when using tkmedit, for example: > > tkmedit subj_name norm.mgz

[Freesurfer] Export Freesurfer labels to SPM ROIs

Hello FS community, I have made some custom labels based on retinotopy data and I wish to export these as SPM ROIs so that I can use some specific tools. I grouped the labels into an annotation file and I used mri_label2vol to convert it into nifti, I then imported it into matlab and I get a

Re: [Freesurfer] temporal lobe pial surface problem

Hi Xiaomin, currently I don't have access to my notes, however, if I remember correctly, you can specify thresholds in mris_make_surfaces for consideration in the surface placement. This obviously works well only if the contrast between WM/GM/CSF is high enough. If you are interested and

[Freesurfer] Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04

Hello, Recently, I started using freesurfer on a Ubuntu system. I've noticed two issues, when using tkmedit, for example: tkmedit subj_name norm.mgz -segmentation aparc.a2009s+aseg.mgz (i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is created, and it can be opened in any image