[Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim

External Email - Use Caution Hi FS developers, I have used mri_glmfit-sim to do multiple comparison like below: mri_glmfit-sim --glmdir lh.thickness.0.glmdir --cache 3 abs --cwp 0.05 --2spaces and in the lh.thickness.0.glmdir/group.diff directory, I got some output

Re: [Freesurfer] Coordinate Transformation

This was a bug in FreeView. If you download version 7, you should see reasonable numbers On 5/4/2020 4:51 PM, Hye Bin Yoo wrote: External Email - Use Caution Dear Dr. Greve, Thanks for your prompt response. That's good to know, and indeed I have seen this page. The confusion came

Re: [Freesurfer] longitudinal trac-all -path exited with error

They are created during the -prior step (last step within -prep), which looks like it didn't complete. You probably also ran out memory in that step and didn't notice. Rerun -prior with increased memory and then try -path again. From:

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I think the latest one, but maybe it'll a good idea to start with the original dicoms and not with the nii. Thanks! Noam From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, May 4, 2020 4:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] Coordinate Transformation

External Email - Use Caution Dear Dr. Greve, Thanks for your prompt response. That's good to know, and indeed I have seen this page. The confusion came because the MNI coordinate I know have an origin at anterior commisure, so the x value should range from neg 90 something,

[Freesurfer] Hippocampus subfields ROI

External Email - Use Caution Hi FreeSurfer experts, I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I can see in the hipposubfields.lh.T1.v21.stats and lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and tail

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I have used that before and it seems to work. What version are you/they using? I remember this kind of problem years ago when FSFAST was using SPM to initialize the registration; at some point SPM changed the interpretation of the coordinates which caused a left-right reversal. On 5/4/2020

Re: [Freesurfer] Coordinate Transformation

The "RAS" in that image refers to scanner RAS (not MNI coords). The "Talarairach" is actually MNI305 (it is called this in version 7 to avoid this kind of confusion). In case you have not seen it, here is a page that may answer more of your questions.

[Freesurfer] Coordinate Transformation

External Email - Use Caution Dear Freesurfer Developers, How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

They are using dcm2niix of MRIcroGL From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, May 4, 2020 2:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch How was the nii created? Ie, how did it go from

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

Uuummm interesting… thanks a lot! I’m still investigating this Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Qi" Reply-To: Freesurfer support list Date: Monday, May 4, 2020 at 14:51 To: Freesurfer

Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

External Email - Use Caution Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below: mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab

Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly? On 5/4/2020 2:49 PM, Mason Wells wrote: External Email - Use Caution Hi, Terminal output is below:

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

External Email - Use Caution Hi Eugenio, Another information: though script exited with errors, all the left hemispheres generated hippoSFVolums and amydNucVolumes as outputs. Missing right hemispheres for all. Best, Qi On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E.

Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

External Email - Use Caution Hi, Terminal output is below: /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

How was the nii created? Ie, how did it go from dicom to nii? On 5/4/2020 1:56 PM, Peled, Noam wrote: We are running a pilot, to try to analyze their epileptic monitoring unit datasets using the Martinos tools (FreeSurfer and MNE) The analysis was on an fMRI nii file, which I checked before

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

We are running a pilot, to try to analyze their epileptic monitoring unit datasets using the Martinos tools (FreeSurfer and MNE) The analysis was on an fMRI nii file, which I checked before running fsFast, and it was LSA. I wouldn't suspect anything is wrong unless I knew how the results should

Re: [Freesurfer] Recon-all exited WITH errors

Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts  mris_anatomical_stats

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I'd need a lot more details. Where they using FreeSurfer? Sometimes the data will go through several conversions and formats before analysis. If the orientation info was lost or changed, then that could explain it On 5/4/2020 1:22 PM, Peled, Noam wrote: Thanks Doug! Good to know that. I

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

Thanks Doug! Good to know that. I realized I had a problem when I got activation on the wrong side (right finger tapping shows activation on the right hemisphere) The analysis was done in another hospital when I just helped them remotely. They told me that their analysis software shows the

Re: [Freesurfer] recon-all and fMRI coordinates mismatch

The actual orientation of the input should not matter as long as the nominal orientation matches the true orientation -- FS automatically handles the orientation correctly. When you ask whether the output will be "in RAS", are you asking whether the left side is truly the left (and right is

[Freesurfer] recon-all and fMRI coordinates mismatch

Hello, After running recon-all on a patient, the resulting T1.mgz coordinates system turned to be LIA. Can I guarantee the recon-all output will be in RAS? I also would like to run FS-FAST on this patient's fMRI task dataset, which is in LSA. Any recommendation what should I do to make sure both

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

External Email - Use Caution Thank you so much ! Best, Qi On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Qi, > > I’m really sorry you’re running into all these problem. > > We’ll look into it and get back to you

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

Dear Qi, I’m really sorry you’re running into all these problem. We’ll look into it and get back to you asap Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Qi" Reply-To: Freesurfer

Re: [Freesurfer] Files generate in the process of "recon-all -autorecon3" are all missing

There is no obvious error in the recon-all file, but it does terminate just after creating a symbolic link. Are sym links possible in the CentOS virtual machine in windows? On 5/4/2020 5:14 AM, Frank Chau wrote: External Email - Use Caution Dear Freesurfer experts, I ran recon-all

Re: [Freesurfer] recon-all

You have two classes and one variable. This means that you will have 4 parameters (betas) to estimate (an offset for each group and an age slope for each group). But you only have four input subjects, so your DOF is 0 On 5/2/2020 7:59 PM, jiahui wrote: External Email - Use Caution

Re: [Freesurfer] -T2pial after white matter edits

Sorry, our interface is a little bit confusing on this. Use -T2 to specify the T2 volume (eg, -T2 /path/to/T2.mgz). To apply the T2 to the pial use -T2pial (without any arguments) On 5/2/2020 7:55 PM, Octavian Lie wrote: External Email - Use Caution Dear All, I ran recon-all on the

Re: [Freesurfer] Question regarding design matrix/fsgd/resulting statistical tests

On 5/2/2020 7:27 PM, Meike Hettwer wrote: > External Email - Use Caution > > Hi doug, thanks for the quick response! > I‘m not quite sure if I‘m getting the second part right- could you please > elaborate a bit what you mean by > „When there is only one numerator DOF, then the sig map

Re: [Freesurfer] segmentHA_T1.sh fails with "Error in myMRIread: temporary directory does not exist"

Dear Soichi, Can you please double check that you’ve got writing permissions on your subject directory? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Soichi Hayashi Reply-To: Freesurfer support

Re: [Freesurfer] TRACULA prep roc error

I suspect that you passed it the name of a dicom directory, instead of a dicom file. Please see step 6 of tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula "If DICOM files are available, you just need to specify the first DICOM file in the series that contains the DWIs,

[Freesurfer] TRACULA prep roc error

External Email - Use Caution Hello team, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. #@# Image corrections Sat May 2 19:57:18 CDT 2020 mri_convert --bvec-voxel

[Freesurfer] segmentHA_T1.sh fails with "Error in myMRIread: temporary directory does not exist"

External Email - Use Caution Hello. I am trying to run segmentHA_T1.sh right after successfully completing recon-all -all I have a freesurfer output directory under my currently working directory inside ./output. So I ran this command. $ segmentHA_T1.sh output . When I do I

[Freesurfer] PhD position at Lund University

External Email - Use Caution Dear all, We have a PhD position available on imaging of the medial temporal lobe in aging and dementia at Lund University, Sweden, with the Biofinder Group. See here for more details and applying: https://lu.varbi.com/en/what:job/jobID:331266 The

Re: [Freesurfer] error while obtaining lGI

External Email - Use Caution Hello! Thank you for the tip! As i understand it, -lGI has only one input which is pial surface. I am running it without any other files in the subject directory, I only have Subject- Name_-Surf- ?h.pial files when I attempt to execute the -lGI on

Re: [Freesurfer] error while obtaining lGI

External Email - Use Caution If you replaced the lh.pial and rh.pial files with different ones generated in another software, the vertex counts in these files will almost certainly not match the number of vertices (and faces) of all the other surfaces generated by FreeSurfer