Re: [Freesurfer] Qdec crash while analysis almost finished

I'm not sure I understand. Are you using v6 qdec with a 5.3 license file? On 1/13/2021 2:54 AM, chenb...@mail.sysu.edu.cn wrote: External Email - Use Caution Hi, dear Freesurfer experts, I recently came across an invalid Freesurfer license key error

Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

, Kevin Date: Tue, 12 Jan 2021 15:45:37 + From: "Greve, Douglas N.,Ph.D." mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0 To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesu

Re: [Freesurfer] matrix is ill-conditioned or badly scaled

NaN will not work for this. You can't do incomplete designs with an FSGD. You can create your own design matrix and pass it with --X, otherwise you'll have to exclude those subjects or put some reasonable (eg, imputed) value On 1/12/2021 6:35 PM, Julie Ottoy wrote: External Email - Use

Re: [Freesurfer] almost empty mask.mgh with glmfit

A 0 value usually indicates a bad or uninterpretable voxel which you would not want to include in your analysis. You can, of course, by not pruning. But I think you need to answer the question as to why the values are 0. Is 0 interpretable in this case? On 1/11/2021 6:15 PM, Julie Ottoy wrote:

Re: [Freesurfer] Non-uniform voxel size

voxel sizes. Or is there perhaps a way to apply the "aparcstats2table -meas volume" command but get the same ROIs outputted as those in the gtm.stats file? Thank you for the info! Julie On Wed, 23 Dec 2020 at 13:11, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: N

Re: [Freesurfer] parcellation-based connectome viewing in freeview.

this might be something you can do in matlab with the function below (found in $FREESURFER_HOME/matlab) function surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile) % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile) % % Example: % I have three annotations %

Re: [Freesurfer] Editing Recon-all on Different Computers

Yes, i think that is still fine On 1/5/2021 8:18 PM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Hi Allison As a follow-up to this question Applying gcut to improve skull stripping when making the manual edits on a different computer be a problem (still same FS version

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD files as found in $FREESURFER_HOME/average/mult-comp-cor On 1/5/2021 4:55 PM, Na, Xiaoxu wrote: External Email - Use Caution Dear Freesurfer Experts, I’ve all the subjects successfully done recon-all, lgi

Re: [Freesurfer] Desikan Killiany Atlas Node Coordinates

If you want the coordinates, you can also run mri_segcentroids on the aparc+aseg.mgz in fsaverage. Or, if you want them in mni152 space, you can run the 152 through recon-all and then run mri_segcentroids on the resulting aparc+aseg.mgz On 1/5/2021 11:01 AM, Mora, Jocelyn S. wrote: Hi Jessica,

Re: [Freesurfer] eTIV=0.0 on volumes where control points have been added manually

Hi Julia, this is a bug. We've fixed it in our development version, but for you there are a few option. One is that you can just get the value from aseg.stats (asegstats2table). Or you can run recon-all with these flags -talairach -parcstats -parcstats2 -parcstats3 On 12/29/2020 7:34 AM, Julia

Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 36 Topic 14. Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory (Greve, Douglas N., Ph.D.)

Sorry, I lost track of the original thread. Can you explain it or say why you are not running recon-all? On 1/4/2021 9:27 AM, Camerino, I.L. (Ileana) wrote: External Email - Use Caution Dear Douglas, Thank you so much for your reply. After trying: mri_em_register -mask brain.mgz -p .5

Re: [Freesurfer] recon-all -hires option

If you want to try to do it systematically, you can add -wsless (should reduce the agressiveness of the skull strip) On 1/4/2021 3:52 AM, falk.luesebr...@med.ovgu.de wrote: External Email - Use Caution Hi Simon, in case your surfaces (and other

Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

For some reason, it is not capturing the terminal output in the log files. Can you just run mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz and send me the terminal output? On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote: Hello

Re: [Freesurfer] The lookuptable value of Virchow–Robin space

Probably 77 WM-hypointensities 200 70 255 0 On 1/2/2021 1:11 PM, Aaron Tanenbaum wrote: External Email - Use Caution Ideally, what should Virchow–Robin space be labeled as. ___ Freesurfer mailing list

Re: [Freesurfer] Transform rescaled non-pvc PET to surface

If you've run mri_gtmpvc already, you can add --save-input and it will save a file called input.rescaled.nii.gz which will be rescaled to your reference region On 12/29/2020 4:19 PM, Julie Ottoy wrote: External Email - Use Caution Dear Freesurfer team, I have a question related to

Re: [Freesurfer] Failed tissue type check {Disarmed}

eft-undetermined It may be that there are no voxels for this seg when mapped into the input space. Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the registration Build time 5.9690, err = 1 Thank you, Julie On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. mailto:

Re: [Freesurfer] Group Analysis Question

I think that contrast computes Female-Male regressing out Dx and age. If you want HC vs MS, then use -0.5 -0.5 0.5 0.5 On 12/29/2020 4:52 PM, Swanson,Clayton wrote: External Email - Use Caution Hi Freesurfer Team, I am performing an analysis on 23 HC and 26 people with MS and I would

Re: [Freesurfer] talairach.lta coordinate spaces

Note that FS will "conform" the volume to be coronal with axes aligned with the major scanner axes, so that will undo a lot/all of your rotation On 12/29/2020 11:37 AM, Fischl, Bruce wrote: > p.s. oh, and the .lta format is ascii so you can just look at it to see if it > is vox2vox or ras2ras >

Re: [Freesurfer] error in running tkregisterfv (Greve, Douglas N., Ph.D.)

Sorry, I deleted the previous emails. Can you repost with our previous exchanges so I know the context? On 12/28/2020 9:30 AM, Peter de Best wrote: External Email - Use Caution Dear Dr. Greve, Thank you so much for the information. However, after adjusting the registration file to

Re: [Freesurfer] Access to datasets used for validation of sbTIV and eTIV measures

ADNI30 is lost by now. For SASHA, we don't have the actual manual labels, but we still have the TIV generated from those labels. I'm pretty sure that we cannot release that data. Sorry, not much luck here On 12/26/2020 2:49 PM, Erus, Guray wrote: > External Email - Use Caution > >

Re: [Freesurfer] segmentation fault

Please send the recon-all.log file On 12/25/2020 8:42 PM, Wei Koo wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon2 for a number of subjects, but one of my subjects I get the following error when I run the mri_tesellate command: Removing

Re: [Freesurfer] Question about a feature introduced in FS 7.0 {Disarmed}

oaseg -autorecon3". I found this to move the surface however the aparc+aseg file had the voxel I altered as 247. Last night I tried what you suggest with the same alterations to the aseg.presurf file, I found the surface and aparc+aseg was unchanged. On Wed, Dec 23, 2020 at 12:28 PM Greve, Dougl

Re: [Freesurfer] Question about a feature introduced in FS 7.0

I don't have any example, but the idea is pretty simple. If you want to freeze a point on the surface, open aseg.presurf.mgz and the surfaces for your subject, eg, tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs Then edit the aseg.presurf.mgz to change the voxels where you want to freeze

Re: [Freesurfer] Error

Source 7.1.1 Go into $SUBJECTS_DIR rm fsaverage ln -s $FREESURFER/subjects/fsaverage that should do it On 12/22/2020 8:47 AM, Weerasekera, Akila wrote: Hello, I sent a few jobs to launchpad (FreeSurfer segmentation) and they exited with an exit=1, this is the error: "ERROR: Label FG1.mpm.vpnl

Re: [Freesurfer] recon labels.DKT31.manual.nii.gz appears ERROR: Talairach failed

Can you send the recon-all.log file? On 12/22/2020 7:23 AM, 1248742467 wrote: External Email - Use Caution Hello, everyone I have download the labels.DKT31.manual.nii.gz in mindboggle datsets, I want to use recon-all command to get lh.labels.DKT31.manual.annot. But, when I run:

Re: [Freesurfer] Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory

Try using RB_all_2016-05-10.vc700.gca instead On 12/22/2020 5:54 AM, Camerino, I.L. (Ileana) wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] No extracerebral CSF in sGTM

yes, it does, assuming the segmenation of extra cerebreal CSF is adequate On 12/22/2020 12:57 AM, Julie Ottoy wrote: External Email - Use Caution Dear Petsurfer team Does the sGTM PVC correct for the uptake in extra cerebral CSF? If not, how would this affect the reliability of the

Re: [Freesurfer] cluster size and FWER rough equivalence?

On 12/21/2020 8:45 PM, Kayle Sawyer wrote: External Email - Use Caution We are working on a manuscript revision for an fMRI project that was analyzed with FS-FAST 5.3 years ago. We used mri_glmfit, and then we ran mri_surfcluster (instead of mri_glmfit-sim) with a vertex-wise

Re: [Freesurfer] Talairach Failure in recon-subject {Disarmed}

That is just the failure detection. Sometimes it generates a false positive. Did you check the transform? If the rest of the downstream processes (eg, aseg and surfaces) are ok, then you don't need to worrry On 12/21/2020 6:53 PM, Wei Shao wrote: External Email - Use Caution Hi,

Re: [Freesurfer] Vertex-wise functional ROI extraction

We don't have anything that creates a text file of the time course in each voxel, if that is what you mean. In principle you can do it in matlab... On 12/21/2020 4:28 PM, Sussman, Lauren wrote: > External Email - Use Caution > > Hello! > > I would like to extract functional data from a

Re: [Freesurfer] Non-uniform voxel size

No, not a problem. On 12/21/2020 12:52 PM, Julie Ottoy wrote: External Email - Use Caution Dear freesurfer team, I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the

Re: [Freesurfer] PFC segmentation

Do you want a binary map? If so, you can run mri_binarize --i aparc+aseg.mgz --o pfc.mgz --match Id1 Id2 ... where Id1 ... is a list of segments you want in your binary map as found in $FREESURFER/FreeSurferColorLUT.txt, eg, 1028 is left superior frontal 1028ctx-lh-superiorfrontal

Re: [Freesurfer] monkey atlas D99 {Disarmed}

lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> ha scritto: Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples On 11/26/20

Re: [Freesurfer] Anterior insula thickness

We don't have an anterior insula segmentation. One thin you can try is to divide the insula label with mris_divide_parcellation. If one of those subdivisions works for you then you can compute the thickness inside it. You might want to do it on fsaverage and then map it back to the individual

Re: [Freesurfer] fspalm contrasts {Disarmed}

Oh, sorry, I did not include that as a possibility. FSL codes F-contrasts differently than t-contrasts (FS codes them in the same way, just a matrix). If you want to do it this way, you'll have to use PALM by itself without the fspalm frontend. fspalm should still create files that can be

Re: [Freesurfer] Error in selxavg3-sess {Disarmed}

Can you send the full terminal output? Do all subjects have the same paradigm files? On 12/21/2020 5:24 AM, Nina Khatibi wrote: External Email - Use Caution No, I have checked them all. On Thu, Dec 17, 2020 at 6:05 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>

Re: [Freesurfer] how to use recon-all command

Try looking at our tutorials on how to get started http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials but you can start by running recon-all -s your-first-subject -i T1.nii.gz -all On 12/21/2020 4:03 AM, 1248742467 wrote: External Email - Use Caution Hello, everyone my freesurfer

Re: [Freesurfer] Can't find Mindboggle datasets

don't know, try asking the people at mindboggle On 12/21/2020 3:40 AM, 1248742467 wrote: External Email - Use Caution Hello, everyone In mindboggle website, the data is freesurfer-output, But I just want to download the 101 source data, use recon -all command preprocess them by myself.

Re: [Freesurfer] Converting a binary volume roi.nii file to a label for roi analysis in Freesurfer

Run recon-all on the MNI template, then view your ROI on the output volume, including the surfaces to verify that the surfaces pass through your ROI. Map the ROI to the surface using mri_vol2surf with the --regheader option, then map the surface-ROI to each subject with mris_apply_reg (make

Re: [Freesurfer] error in running tkregisterfv

tkregisterfv requires an LTA file. Try running bbregister with an LTA output, eg, bbregister --s subject_30_8_2020 --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.lta --init-header –bold On 12/20/2020 5:03 AM, Peter de Best wrote:

Re: [Freesurfer] Failed tissue type check {Disarmed}

You can use the fix from my previous email or you can add the following line any were into the gtmseg.ctab file: 29 Left-undetermined 135 206 235 0 3 On 12/18/2020 11:06 PM, Julie Ottoy wrote: External Email - Use Caution Sorry I would like to correct my

Re: [Freesurfer] Failed tissue type check {Disarmed}

Try adding --replace 29 2 to your command line On 12/18/2020 12:07 AM, Julie Ottoy wrote: External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to

Re: [Freesurfer] error message when running mri_info

You can see that the vox_units are Unknown in the fslhd output. This is the source of the problem in FS. On 12/18/2020 10:53 AM, Jonathan Lynn wrote: External Email - Use Caution Hello, I've been using a software to process SWI data that includes an option to save the output as nifti

Re: [Freesurfer] Extracted mean timecourse from FS label {Disarmed}

vard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: Thursday, December 17, 2020 2:20 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:free

Re: [Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

Is the lh.orig surface changing? On 12/17/2020 5:53 PM, Ben Deen wrote: External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to

Re: [Freesurfer] Multiple Frames

What are the 2 frames? You could extract the first or the second or average them or compute an RMS, but it depends on what is there On 12/17/2020 2:03 PM, Hsieh, Stephanie wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FREESURFER AND NEURONAVIGATOR IMAGE

Sorry, we don't have anything that will do this. I know there are a few out there that will do it, but I don't know their names off hand. Maybe 3D slicer. On 12/17/2020 4:20 AM, marco.m...@tin.it wrote: External Email - Use Caution I need to use freesurfer

Re: [Freesurfer] fspalm error : --sig2p-max unknown

You need the patch. See the docs here https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm under Setting Up On 12/16/2020 2:02 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, When I was running permutations with fspalm an error appeared because it couldn't find the

Re: [Freesurfer] Error During Fix Topology and Brain Usability

I don't think it is worth doing a surface-based analysis on this subject. The subcortical may be salvageable On 12/16/2020 11:55 AM, Angel Hammond wrote: External Email - Use Caution Dear Experts, I have a brain that I have been getting an error for during fix topology during

Re: [Freesurfer] How to remove clusters less than 50 vertex/voxels in FreeSurfer during visualisation

You can add --minarea XXX to your mri_surfcluster command line where XXX is the minimum area in mm2 On 12/15/2020 8:33 AM, Sunil Khokhar wrote: External Email - Use Caution Dear Experts! After doing the statistics I want to remove clusters that are less than 50 voxels/vertices from

Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

Hard to say without the recon-all.log file, but my guess is that something is wrong with one of your surfaces. Load the surfaces in freeview and see how they look On 12/14/2020 7:30 PM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Hi there, Hope this finds you well I

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

There have been some changes that are breaking your stream. Try this cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh

Re: [Freesurfer] asegstats2table

If you use mris_anatomicalstats to create the stats file (in the stats folder), then use aparcstats2table to create a table from multiple subjects On 12/11/2020 6:57 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Hello Freesurfers, I have a question about the command

Re: [Freesurfer] group analyses

yes, run mris_preoproc with --meas volume, then surf2surf. Then run mri_segstats --i lh.volume.mgz --exludeid 0 --seg ocn.mgz --avgwf avgwf.dat --accumulate where lh.volume.mgz is the output of rerunning mris_preproc above ocn.mgz is the ocn file which is output from the cluster analysis

Re: [Freesurfer] group analyses {Disarmed}

, 2020 at 9:59 AM Sara Lyn mailto:saralyn...@gmail.com>> wrote: Hi Thank you for your response. How do I correct this extracted volume for intracranial volume (etiv)? Thank you Sara On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote:

Re: [Freesurfer] group analyses {Disarmed}

(etiv)? Thank you Sara On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: When you run the thickness analysis with multiple comparisons correction (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the signif

Re: [Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3

The GPU stuff may or may not work. It was hard to maintain because the GPUs kept changing so much, and it would not surprise me that the code from 5.3 is incompatable with GPUs today. But it looks like the error is that it could not find a file. Does that file actually exist? On 12/12/2020

Re: [Freesurfer] Error in selxavg3-sess

Are there presentations that are simultaneous? On 12/12/2020 3:19 AM, Nina Khatibi wrote: External Email - Use Caution Hi, I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each subject contains 15 runs, I've done plenty of analyses with different paradigm

Re: [Freesurfer] HCP_1200 parcellation problems

Sorry, I can't tell from your email what the problem is. Can you elaborate? On 12/9/2020 2:30 PM, najme soleimani wrote: External Email - Use Caution Dear FreeSurfer Developers, I downloaded the HCP_1200 subjects' structural extended data. I am attempting to have equal sized

Re: [Freesurfer] need assistance to decode QDEC results

It depends on the order that you specified them. You will have four groups SczUrban SczRural HVUrban HVRural The interaction will be of the form (SczUrban-SczRural)-(HVUrban-HVRural) Look in the y.fsgd to see what the order of the classes is. You can then look in the contrast folder at C.dat

Re: [Freesurfer] MP2RAGE pial surface edit error

Essentailly, this is a skull strip error, so you may need to remove the skull (ie, non-brain) manually On 12/9/2020 6:25 AM, Elisa Rehbein wrote: External Email - Use Caution Dear Freesurfer experts, we are currently running recon-all for our MP2RAGE images, using Freesurfer 7.

Re: [Freesurfer] Extracted mean timecourse from FS label

I don't know, that msg probably comes from the gifti code we link to. It looks like it is just a warning. Do the output waveforms look ok? On 12/9/2020 6:05 AM, Mason Wells wrote: External Email - Use Caution Hi Experts, I have pre-processed some resting-state date using fMRI prep. I

Re: [Freesurfer] labels in the surface

This might be the way it is given that the AAL is volume-based and you are trying to put it on the surface. What is your vol2surf command? On 12/10/2020 6:59 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Hello Freesurfer team With your help i obtained a AAL atlas on

Re: [Freesurfer] Computing thickness from woT2.pial surfaces

If you're using v7XX, then you can use mris_place_surfaces. Look in the log file for the command line. On 12/9/2020 6:15 AM, Antonín Škoch wrote: External Email - Use Caution Dear experts, I have processed my data with -T2pial option. I would like now to also compute thickness from

Re: [Freesurfer] Does segmentation depend on input orientation {Disarmed} {Disarmed}

How did you change the orientation? On 12/9/2020 4:16 AM, Nederpelt, D. van (David) wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] question about PVC of PETSurfer {Disarmed}

to know not only how to use the image after PVC, but also where to find the 3D image in the folder? On 11/30/2020 01:14，Greve, Douglas N.,Ph.D.<mailto:dgr...@mgh.harvard.edu> wrote： It is not set up to use the subfields. In principle it could be, but I don't think it would be very accurate b

Re: [Freesurfer] Correct for sulcuses & ventricles size

On 7/11/2018 11:37 AM, John Anderson wrote: External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space

Re: [Freesurfer] inflated surface with holes

Ths is a topological error that can be fixed with mris_fix_topology. But this does not look human ... On 12/8/2020 3:34 PM, Jie Zhao wrote: External Email - Use Caution Hello Freesurfer Team I have some questions about the inflated surface. As is shown in the attached pictures,

Re: [Freesurfer] recon-all error {Disarmed}

Does it work on other subjects? I'm guessing this has to do with having the MNI tools properly installed. For testing purposes, can you download and run version 7 to see if it works? On 12/8/2020 12:40 PM, Devanshi jain wrote: External Email - Use Caution Hello FreeSurfer Developers,

Re: [Freesurfer] group analyses {Disarmed}

When you run the thickness analysis with multiple comparisons correction (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the significant areas. You can use this to extract other information. If you want volume, then run mris_preproc using the --meas volume flag, the

Re: [Freesurfer] convert to native space

On 12/5/2020 2:16 AM, Wei Shao wrote: External Email - Use Caution Hello, Freesurfer team This is Wei Shao, I was trying to convert the freesurfer automatic segmentation of the hippocampus subfield into native space so I can compare it with the manual segmentation. Here is the

Re: [Freesurfer] PVE correction tool Petsurfer {Disarmed}

They smooth by 8mm post processing and do allow you to have the unsmoothed images? Sigh. The best thing to do is to use sqrt(psf1^2+psf2^2) where psf1 is the psf of the scanner and psf2 is 8mm. psf1 is probably about 6mm. Which version of ADNI is this? On 12/4/2020 5:42 PM, Julie Ottoy wrote:

Re: [Freesurfer] flipped_hemisphere

Did you put a fiducial on your subject to mark left and right. If not, whey do you suspect the results are flipped? Did you use dicom file or did you convert them to something else before running recon-all? On 12/3/2020 12:31 PM, Mora, Jocelyn S. wrote: Hi, If you are interested in checking

Re: [Freesurfer] Does segmentation depend on input orientation {Disarmed}

Yes, this can happen (and happens to almost all neuroimaging packages). As with any optimization program, where it ends up depends a little on where it starts. On 12/3/2020 6:31 AM, Nederpelt, D. van (David) wrote: ___ Freesurfer mailing list

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

hould I do if there is something wrong -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu> 发送时间:2020-11-30 01:22:22 (星期一) 收件人: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.

Re: [Freesurfer] Aligning functional and structural scans with FsFast

Do you mean you want to register the fMRI data to the anatomical? If so, use bbregister. If you've run the fMRI through FEAT, then pass the template to the --mov flag On 12/1/2020 10:46 PM, Karan Desai wrote: External Email - Use Caution Hi FreeSurfer developers, I have Freesurfer

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

What are you using to compute the significance of the difference using the ROI average? On 11/30/2020 7:59 PM, 李梦君 wrote: External Email - Use Caution Yes, what should I do if there is something wrong -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harv

Re: [Freesurfer] mri_surf2surf lh.area does not match surface (148208, 146833)

It looks like you edited the subject but did not fully re-run it. Try recon-all -s HLN-12-2 -autorecon3 On 12/1/2020 4:01 AM, 1248742467 wrote: External Email - Use Caution Hello, Fs When I run the following command: mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv

Re: [Freesurfer] Fwd: Issue with custom label

Try --i mri/aparc+aseg.mgz instead of --c On 11/30/2020 7:28 PM, Catherine Tallman wrote: External Email - Use Caution Hello, I was wondering if there were any updates on this question? Thank you, Catherine -- Forwarded message - From: Catherine Tallman

Re: [Freesurfer] About mri_vol2surf {Disarmed}

subject in my study. Is this the correct workflow? El lun, 30 nov 2020 a las 16:26, Greve, Douglas N.,Ph.D. (mailto:dgr...@mgh.harvard.edu>>) escribió: Oh, don't use .img as it cannot handle the surface dimensions. Technically, nifti cannot either, but I hacked our nifti version to accom

Re: [Freesurfer] Multiple regression analysis

good question. I don't think there is anything wrong with multiplying two zs, but it might be more appropriate to multiply the raw covariates and then compute a z from that. On 11/30/2020 4:07 AM, Marina Fernández wrote: External Email - Use Caution Dear all, I am doing a multiple

Re: [Freesurfer] About mri_vol2surf {Disarmed}

continue with the image in this format? What's the difference that makes this error appear with .img format? El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D. (mailto:dgr...@mgh.harvard.edu>>) escribió: Can you send the full terminal output? On 11/18/2020 6:41 AM, Alberto Del Cerr

Re: [Freesurfer] mri_surf2surf Cannot allocate memory

How was lh.sphere.reg created? It might be corrupted, so try creating it again. On 11/30/2020 3:11 AM, 1248742467 wrote: External Email - Use Caution Hello,Fs When I used mri_surf2surf command to template the lh.thickness to fsaverage5 space, the error appeared: Command: mri_surf2surf

Re: [Freesurfer] what command can be used to template .vtk file to fsaverage5 space?

what space is the vtk surface in? On 11/30/2020 2:55 AM, 1248742467 wrote: External Email - Use Caution Hello, what command can map VTK file to fsaverage5 space? I want its vertex number to be 10242. If you know, please give me an example. Looking forward to your reply

Re: [Freesurfer] extracting mask for basal ganglia, deep grey, and centrum semiovale

We don't have a centrum semiovale label in FS. You could try using the (Left,Right)-UnsegmentedWhiteMatter in the wmparc.mgz On 11/27/2020 9:28 AM, miracle ozzoude wrote: External Email - Use Caution Hello Experts, I did like to create a mask for basal ganglia, deep grey matter, and

Re: [Freesurfer] Mean Curvature

I don't know. I've never seen this type of analysis. I think with and without would be valid analyses, but they would be answering different questions, so, as the scientist doing the study, it is more up to you. On 11/27/2020 8:56 AM, Letitia Schneider wrote:

Re: [Freesurfer] mri_segstats question

v 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. >> wrote: >> >> I don't understand why WM was cropped out. What command were you trying >> to use? >> >> On 11/18/2020 2:39 AM, RENXI LI wrote: >>> External Email - Use Caution >>>

Re: [Freesurfer] monkey atlas D99

Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples On 11/26/2020 9:16 AM, Francesca Strappini wrote: External Email - Use Caution Dear FreeSurfer experts, I'm trying to

Re: [Freesurfer] error: MatrixMultiply: m1 is null {Disarmed}

Not in FS. Try using dcm2niix On 11/26/2020 5:07 AM, John Papatriantafyllou wrote: External Email - Use Caution Hi freesurfer exps, last year a recieve dicom 3d as one file (300 dicoms one file) Is there any program to unpack them or any other way to recon all John

Re: [Freesurfer] (no subject)

No, you'll have to add it as a covariate. Or you can add --etiv when you run mris_preproc and it will divide the maps by the eTIV On 11/25/2020 3:23 PM, Sara Lyn wrote: External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if

Re: [Freesurfer] Mean Curvature for whole hemisphere

No, probably just an oversight On 11/25/2020 10:06 AM, Josue Luiz Dalboni Da Rocha wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PETSurfer voxelwise statistic

Traditionally, MG analysis is only run on GM. In principle, it is possible to run it on WM, but we don't offer that as an option. On 11/25/2020 8:16 AM, Boris Rauchmann wrote: External Email - Use Caution Dear all, How can I run a voxelwise statistic using grey and white matter

Re: [Freesurfer] Splitting a label region?

Try mris_divide_parcellation Run with --help to get docs On 11/25/2020 1:57 AM, Hyon, Justin J. wrote: > External Email - Use Caution > > Hello, > I am wondering whether there is a way to split a labeled region in a volume > into 2 labels, perhaps by using the Freeview gui? I just need

Re: [Freesurfer] group analysis

For starters, you need to have four classes, HC-Male, HC-Female, CMT-Male, CMT-Female and not use gender as a variable. Try that. I would also normalize the age and thickness On 11/24/2020 12:04 PM, Ambulatorio SNA FEDERICO II wrote: External Email - Use Caution Dear Freesurfer team,

Re: [Freesurfer] Manual ROIs in PETSURFER

It is, but it can be either easy or hard. The easy way is to draw it on gtmseg.mgz and add an entry into gtmseg.ctab. Probably, you should copy the gtmseg.{mgz,ctab} to a new file and edit that. Otherwise, you can edit, eg, apas+head.mgz, and pass that to gtmseg with the --head option. At some

Re: [Freesurfer] mri_surf2surf (and mri_preproc) clarification

I think that would be ok, but I would run this instead mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type curv --cortex --trgsubject fsaverage5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10 On 11/23/2020 4:11 PM, Daniel Leopold wrote:

Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

If you want a cluster table, then you will have to run mri_surfcluster on the output of the conjunction. Run it with --help and write back if you need more info On 11/21/2020 10:03 AM, Paula Maldonado wrote: External Email - Use Caution Dear Douglas, Could you please tell me where

Re: [Freesurfer] PETSurfer

One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ... Otherwise, you can run fscalc, eg, fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o mgx.ctxgm.rescaled.nii.gz On 11/20/2020 11:44 AM, Boris Rauchmann wrote: External Email - Use Caution Dear

Re: [Freesurfer] Time required to run permutations

This might be a bug with the --bg option when 1 is specified. Try it without --bg or try it with 2 or more threads On 11/20/2020 10:20 AM, Basavaraju, Rakshathi wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs

It is probably easier to just run recon-all on the mni152, then use mri_segcentroids on aparc.a2009s to extract the centroids On 11/20/2020 2:50 AM, Hengameh Marzbani wrote: External Email - Use Caution Hello Freesurfer developers, For the purpose of reporting ROIs in my article, I

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