[Freesurfer] Using mri_surf2surf to split files

External Email - Use Caution Hi FreeSurfer developers, I have preprocessed files in single niftis and would like to split the data for each file into left and right hemispheres to run it through a specific toolbox. It seems like there should be a way to run mri_surf2surf or

[Freesurfer] cerebellar parcellation using the Buckner2011_17Networks atlas

External Email - Use Caution Dear expert, I am Anna, a medical school student at Pusan national University, Korea. I am writing this email because I'd like to ask you questions. I would like to measure the cerebellar gray matter volume parcellated using the

Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

External Email - Use Caution Or, are you saying that I do not need to turn it off for NHP? Get Outlook for

Re: [Freesurfer] Cerebellar Segmentation Definitions

Yes On 1/26/2021 11:58 AM, Horn, Mitchell Jacob wrote: Hi Doug, Thanks for your reply. Would it be safe to say that these deep grey nuclei are included in the cerebellar white matter? Thanks, Mitch ___ Freesurfer mailing list

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

By default, mri_glmfit-sim will compute a spatial average inside of a cluster to create the OCN table, so the values do not agree with the table below. In he case of area or volume inputs, it needs to compute the sum instead of the average. I have just modified this program to do this. I've

Re: [Freesurfer] question on data quality - examples in appendix

On 1/26/2021 3:18 PM, Nils B. wrote: External Email - Use Caution Hello everyone, I'm analyzing 1,5T scans and I've two problems with the data quality of my participants, where I hope you can help me. 1. In two of my scans the participants have blurry areas near the cerebellum,

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

But the question I have is why you want to do that? On 1/26/2021 10:48 AM, Trisanna Sprung-Much wrote: External Email - Use Caution Hi Doug We want the surfaces to be extracted from volumes that have been registered to MNI152, rather than extracting the surfaces in the native space

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi there As a follow-up to this, I downloaded one file to test things and it seems the .gii surface files cannot be read by Freeview 7.1: mrisReadGIFTIfile: GIFTI file

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Matt Great, I will check out all the folders. Just made an account now. By "paint surfaces" I mean create/edit labels on the surfaces, specifically related to sulci. best Trisanna From:

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

Okay, maybe it’s a permission error. How about the output of the following? touch /tmp/mytempfile && rm -f /tmp/mytempfile Also, are you running recon-all on a cluster? Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Loreto, Flavia Date: Tuesday, January 26, 2021 at

Re: [Freesurfer] Saving more than one figure using freeview

Hi Noam, You can’t save multiple figures with one -ss flag. If you want to save multiple screenshots without having to load the volume every time, you can write a series of command lines in a text file like this: freeview foo.mgz -viewport x -ss pic1.jpg -viewport y -ss pic2.jpg -viewport z

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Sorry I’m completely confused now about what you are trying to do. The data in ${StudyFolder}/${Subject}/T1w is also in MNI space, but after only a 6 DOF rigid registration (i.e. no changes in brain shape, just a similar brain orientation and AC at

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Thanks for this Matt. Just a question – is it called “MNINonlinear” because a non-linear registration was used to MNIspace? If this is the case, I would prefer to paint in the subject’s native space. Best, Trisanna Sprung-Much Research Associate

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Right just use the surfaces in ${StudyFolder}/${Subject}/MNINonLinear. These are in MNI space and should work for you. They are in GIFTI format, which is readable by FreeView. In the future, it is trivial to move surfaces to MNI space after they

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

External Email - Use Caution Hi Andrew, Many thanks for your reply. This is what I get if I ls/temp: -bash-4.2$ ls /tmp hsperfdata_gc520 hsperfdata_rf1116 hsperfdata_scliffor pbs.3000969.pbs systemd-private-845d4b93c36041db9cb4f47a494a5f87-httpd.service-gKdDDc

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Sure. Give it a try and if something fails we can see about fixing it Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trisanna Sprung-Much Sent: Tuesday, January 26, 2021 1:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Bruce Thanks for your speedy response. This would be an immense time saver if this works. I will give this a go. Yes, you are correct about the blurring as well! Best Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Hi Trisanna Yes, I’m pretty sure that would work. That is, using the current freeview on older versions of recon data. Cheers Bruce p.s. one addendum – you should not have to blur the labels after registration, assuming your manually labeled dataset is big enough From:

[Freesurfer] Saving more than one figure using freeview

Hello all, Can I use the -ss flag in freeview to save more than one figure? Currently, I'm calling freeiew 3 times, each time with a different viewport (sagittal, coronal, and axial) Thanks, Noam ___ Freesurfer mailing list

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Matt OK, I think there has been some confusion and I think I just realized what it is. I am from the MNI and we are used to using the ICBM database, not HCP database. We are also used to painting sulci in volumetric form, so we always used to

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

External Email - Use Caution To make it clear, I would like to extract the area of each subject in the cluster. May I know if this is the correct way? If not, it's appreciated if you would point it out. Thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Na,

[Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

Hi Flavia, Do you have access to /tmp on your system? Can you `ls /tmp`? Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Loreto, Flavia Date: Tuesday, January 26, 2021 at 11:29 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: T1 Recon-all error:

Re: [Freesurfer] Cerebellar Segmentation Definitions

Hi Doug, Thanks for your reply. Would it be safe to say that these deep grey nuclei are included in the cerebellar white matter? Thanks, Mitch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] monkey atlas resampling

External Email - Use Caution Dear FreeSurfer experts, I'm trying to resample an anatomical monkey atlas D99 to the functional space. I run this command line: mri_vol2vol --reg registerNMT2toCassis.dat --mov D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --targ

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

External Email - Use Caution Hi Douglas, Here is the result: -bash-4.2$ ls -l /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot -rw-rw 1 floreto rds-000730 925609 Jan 17 04:02

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

Sorry, that first one should have been ls -l /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot left off the "t" On 1/26/2021 10:55 AM, Loreto, Flavia wrote: External Email - Use Caution Dear Douglas, Thanks for your reply. Please see below the results of

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution I think it would be a good idea to take a step back and tell us what you are trying to accomplish. This is all not the right way to go about things. The HCP already produces surfaces registered to MNI space in the volume for example. Matt. From:

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Matt We want the surfaces to be extracted from volumes that have been registered to MNI152, rather than extracting the surfaces in the native space of the subject, which is what FreeSurfer does. I have done this for 2 other projects in the past

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Doug We want the surfaces to be extracted from volumes that have been registered to MNI152, rather than extracting the surfaces in the native space of the subject, which I remember you saying at a workshop a few years ago is what FreeSurfer

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Please explain what you are doing that requires this. There are many good reasons why this is not the approach FreeSurfer or the HCP have taken. Not the least of which is that all volumetrics and morphometrics will be invalid if not measured in

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

External Email - Use Caution Dear Douglas, Thanks for your reply. Please see below the results of those commands: -bash-4.2$ ls -l /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno ls: cannot access

Re: [Freesurfer] ROI Correlations

External Email - Use Caution Thanks, I will let you know if I can make it work. On Jan 26, 2021, at 8:25 AM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: The only thing I have that I think will do what you want is a matlab script (annotval2surfoverlay.m, attached);

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution That’s not a good idea either. Matt. From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, January 26, 2021 at 9:30 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

It throws an error when trying to extract the bvals or bvects. Can you try it with --no-dwi and see if it runs to completion? If it does, do you have another way to get the bvals and bvects? On 1/26/2021 3:33 AM, Hannah Eichhorn wrote: External Email - Use Caution Thanks for your

Re: [Freesurfer] question on GLM

0 0 0 0 0.25 0.25 0.25 0.25 will do it On 1/26/2021 9:44 AM, Barletta, Valeria wrote: Thanks. And what about the effect of age? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

Re: [Freesurfer] Help with mergecontrasts-sess function

They way you have specified your contrast is a conjunction of individual contrasts, ie, cA>cAc AND cB>cBc. If that what you want? Originally, you were just asking about  the interaction On 1/26/2021 5:17 AM, Paula Maldonado wrote: > External Email - Use Caution > > Thanks for your

Re: [Freesurfer] FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

please send the result of ls -l /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.anno ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001/label ls -ld /rds/general/project/imperialapc/live/freesurfer/APC001 ls -ld /rds/general/project/imperialapc/live/freesurfer

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Why are you registering it to the MNI prior to FS analysis? On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote: External Email - Use Caution Hi Doug and Matt So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and have been registered to our 0.5mm MNI152

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution You are likely to get significantly worse results by reprocessing the HCP subjects with FreeSurfer 7.X. Unfortunately it has issues with HCP data that haven’t been addressed yet. Matt. From: on behalf of Trisanna Sprung-Much Reply-To:

Re: [Freesurfer] ROI Correlations

The only thing I have that I think will do what you want is a matlab script (annotval2surfoverlay.m, attached); copy it to $FREESURFER/matlab There is documentation in the file on how to run it. Can you look at that and see if you can make it work? On 1/26/2021 9:39 AM, Swanson,Clayton wrote:

Re: [Freesurfer] lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview

They would be different. V7 works differently than previous versions in this way to allow for cases where the pial is placed using T2 instead of T1 On 1/26/2021 8:32 AM, Erika Nolan wrote: External Email - Use Caution Goodmorning Dr. Greve, Thank you for responding. The symbolic

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution Hi Doug and Matt So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and have been registered to our 0.5mm MNI152 template, to avoid losing data by registering to the 1mm template. That's all. As for the recon-all.log,

Re: [Freesurfer] ROI Correlations

External Email - Use Caution Hi Doug, Thanks for getting back to me and sorry for not being more clear. I am trying to associate TMS related inhibitory measures to the left pre- and paracentral gyrus thickness for two different groups (healthy, MS). Additionally, I am

Re: [Freesurfer] question on GLM

Thanks. And what about the effect of age? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, January 25,

Re: [Freesurfer] dt_recon error: dimension mismatch between y and X

Hello Antti, It may be possible that you’ve run out of space and the full volumes were not written. You can check by using: df -h /path/to/file Similarly, you can run mri_info on the input files to see how many frames there are and where the discrepancy between the volumes set to x and y are

Re: [Freesurfer] lh.pial and rh.pial ALIAS, become lh.pialT1 and rh.pial T1 in Freeview

External Email - Use Caution Goodmorning Dr. Greve, Thank you for responding. The symbolic links should not be a problem if the .pial and .pialT1 files are essentially the same. If they were to come out as distinct files ( .pial not being a symbolic link for .pialT1), would

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

External Email - Use Caution Thanks for your answer! The full command line is: mri_convert /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA

Re: [Freesurfer] Help with mergecontrasts-sess function

External Email - Use Caution Thanks for your reply, However I have now a doubt regarding one aspect that I had not noticed before. What I wanted to do is to perform the contrast (condA>condAcontrol)>(condB>condBcontrol) with the order of my condition being condA, condAcontrol,