Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Foucault, In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}). There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an

[Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Dear Freesurfer experts, Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/07.html , I wrote a short script to extract the centroids from Desikan-Killiany atlas. ## for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir

[Freesurfer] Freeview mac OSX firewall setting

Dear all, Has anyone using mac OSX experienced constant popping-up of a window asking firewall setting every time when you open FreeView although you have already set it? It's not critical but kind of annoying... so hope you one of you already solved it. Best, -- Seung-Goo ("SG") KIM, Ph.D.

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

Hi Bruce, This is the sequence details: - Axial FLAIR: Plane=AXIAL; Acquisition Type=2D; Coil=8HRBRAIN; Field Strength=3.0 tesla; Flip Angle=90.0 degree; Manufacturer=GE MEDICAL SYSTEMS; Matrix X=256.0 pixels; Matrix Y=256.0 pixels; Matrix Z=42.0 ; Mfg Model=Signa HDxt; Pixel Spacing

Re: [Freesurfer] FsFastPreProc Registration of files from each session to their session's structural image

Yes, it can easily align fmri and and structurals from a different scanner. For the record, FSL can too, they are just being very, very conservative. On 02/20/2018 05:38 PM, Ben Smith wrote: > Thanks - I very much appreciate your thorough explanation! > > We don't expect changes in the actual

Re: [Freesurfer] Fwd: Subjectwise extraction from ROIs

On 02/20/2018 05:54 PM, Sahil Bajaj wrote: > Dear Dr. Greve, > > I have following follow-up questions ('red' colored) for you and would > really appreciate any help. > > On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve > > wrote: > >

[Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 should be compatible with CentOS 7. However in the official documentation I cannot find any related statement. Moveover, the download web page still shows only CentOS 6 as supported platform. Could you please clarify if

Re: [Freesurfer] Fwd: Subjectwise extraction from ROIs

Dear Dr. Greve, I have following follow-up questions ('red' colored) for you and would really appreciate any help. On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve wrote: > sorry for the delay, thanks for reposting > > > On 02/20/2018 11:33 AM, Sahil Bajaj wrote: > >

Re: [Freesurfer] FsFastPreProc Registration of files from each session to their session's structural image

Thanks - I very much appreciate your thorough explanation! We don't expect changes in the actual structure of the brain, but I am concerned about alignment of the structure in 3D space within the scanner. You're probably aware that when using software like FSL, it is typically advisable to align

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

I see , so volumes are also surface based. On Tue, 20 Feb 2018 at 23:16, Douglas N Greve wrote: > so this is thickness data? Hippocampus is a volume-based structure and > so not represented on the surface > > > On 02/20/2018 05:13 PM, amirhossein manzouri wrote: > >

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

so this is thickness data? Hippocampus is a volume-based structure and so not represented on the surface On 02/20/2018 05:13 PM, amirhossein manzouri wrote: > Hi , > This is the output of long_mris_slopes! > > On Tue, 20 Feb 2018 at 23:10, Douglas N Greve >

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

Hi , This is the output of long_mris_slopes! On Tue, 20 Feb 2018 at 23:10, Douglas N Greve wrote: > where did lh.testretest.volume-spc-10.stack.mgh? If this is an fsfast > output, then use the aseg.mgz in fsaverage/mri.2mm > > > > On 02/16/2018 05:24 AM, amirhossein

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

where did lh.testretest.volume-spc-10.stack.mgh? If this is an fsfast output, then use the aseg.mgz in fsaverage/mri.2mm On 02/16/2018 05:24 AM, amirhossein manzouri wrote: > Hi, > To make the mask: > mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh > > Run glmfit: > > cmdline mri_glmfit.bin

Re: [Freesurfer] FsFastPreProc Registration of files from each session to their session's structural image

If you are combining the T1 images together in recon-all, then it is not possible to separate them in FSFAST. If you do not expect structural changes, then you can just register both fMRI sessions to the single anatomical. If you are expecting changes, then analyze the T1 images separately (in

Re: [Freesurfer] Surface Errors

sorry, what kind of errors? I could not really tell from the images what the problem was On 02/20/2018 10:22 AM, Emily Schwartz wrote: > Hi FreeSurfer community, > > I am working on elderly subjects and have had this kind of surface error > quite often in different locations. Usually, it's

Re: [Freesurfer] Fwd: Subjectwise extraction from ROIs

sorry for the delay, thanks for reposting On 02/20/2018 11:33 AM, Sahil Bajaj wrote: > Hello everyone, > > I was wondering if someone could please help me in figuring out > following issues. > > Thanks a lot, > Sahil > -- Forwarded message -- > From: *Sahil Bajaj*

[Freesurfer] mri_robust_template output data size

Hello, Synopsis I have 5 longitudinally acquired high-res volumes at 0.8 mm isotropic resolution. The matrix size is 320x320x240 (240 is long left-right), covering an FOV of 256x256x192 mm3. I've used mri_robust_template to create a template out of these 5 volumes, preferably at the same

Re: [Freesurfer] Goodness of fit

Great. Thank you very much. On Tue, Feb 20, 2018 at 11:19 AM, Douglas N Greve wrote: > I don't output a variance explained per se. You can get p-values > (sig=-log10(p)) and partial correlation coefficient (pcc) for a given > regressor or contrast > > > On 02/20/2018

Re: [Freesurfer] Goodness of fit

I don't output a variance explained per se. You can get p-values (sig=-log10(p)) and partial correlation coefficient (pcc) for a given regressor or contrast On 02/20/2018 12:07 PM, Sarah Cole wrote: > Hi Doug, > > > I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there > is

[Freesurfer] Goodness of fit

Hi Doug, I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there is any way to check the variance explained and fits on the model? Thank you, -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Error in running make_average_subject

Thanks, Andrew! On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew wrote: > Hi Scott, > > It looks like the mri_aparc2aseg binary in that patch directory was > compiled for centos. The version at the following link was compiled on OS > X:

Re: [Freesurfer] Error in running make_average_subject

Hi Scott, It looks like the mri_aparc2aseg binary in that patch directory was compiled for centos. The version at the following link was compiled on OS X: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg If you download this new mri_aparc2aseg

Re: [Freesurfer] Error in running make_average_subject

Thanks andrew... I will try this From: Hoopes, Andrew Sent: Tuesday, February 20, 2018 8:55:47 PM To: M Janani; Freesurfer support list Cc: Sasikala Sethu Subject: Re: [Freesurfer] Error in running make_average_subject Hi Janani, We have

[Freesurfer] Fwd: Subjectwise extraction from ROIs

Hello everyone, I was wondering if someone could please help me in figuring out following issues. Thanks a lot, Sahil -- Forwarded message -- From: Sahil Bajaj Date: Thu, Feb 15, 2018 at 3:50 PM Subject: Subjectwise extraction from ROIs To: Freesurfer

Re: [Freesurfer] Segmenting the Corpus Callosum

Hi Doug check out mri_cc and the help from it. I think you want -t and -d. Probably easiest to run it after recon-all. cheers Bruce On Tue, 20 Feb 2018, Douglas Merkitch wrote: > Hey Bruce, > Could you elaborate on what steps you would need to change the number of > corpus callosum segments

Re: [Freesurfer] Error in running make_average_subject

Hey Andrew, I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as Janani, so I installed this patch. However, now I am getting the following error: #@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018 /Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av \n

[Freesurfer] Requesting to unsubscription

Dear Admin , Can you please remove me from the mailing list of freesurfer. With warm regards Neha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

Re: [Freesurfer] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST

Hi Eric the easiest thing would be to give your n4-corrected image to recon-all and let it run n3 on it. N3 is pretty gentle so I would think this would be fine. The alternative would be harder I think cheers Bruce On Tue, 20 Feb 2018, Axelson, Eric D wrote:   We are using N4 to

Re: [Freesurfer] mris_flatten error: bad vertex

Hi Foteini we need a lot more information. How did you create the patch? What was your command line and full screen output? What version of FS are you using? cheers Bruce On Tue, 20 Feb 2018, Foteini Protopapa wrote: > Dear FreeSurfer Experts, > > > Can somebody tell me if there is a solution

Re: [Freesurfer] Freesurfer Recon all {Disarmed}

and can you give us details of your FLAIR acquisition? What are the voxel sizes? What sequence? On Tue, 20 Feb 2018, Shim Hee Youn wrote: > Hi Bruce, > > Thanks for your email. I am using Freesurfer version 6 and the command I > used to run is this: > > qsub -m n -o o -e e -V recon-all -subjid

Re: [Freesurfer] V6.1

Sorry, we do not have any plans right now to have a new release On 2/20/18 3:23 AM, Eduard Vilaplana Martinez wrote: > Dear freesurfer experts, > > Some days ago I unexpectedly found a thread (about including the flair in the > pipeline) in which you mentioned the v6.1. In my lab we are

Re: [Freesurfer] Segmenting the Corpus Callosum

Hey Bruce, Could you elaborate on what steps you would need to change the number of corpus callosum segments (and grow them laterally), and how to specify the outputs name/format/location? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center On Feb 19,

Re: [Freesurfer] Error in running make_average_subject

Hi Janani, We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ The second part of the readme file in that directory provides instructions for resolving this. best Andrew On February 19, 2018 at 9:40:22 AM, M Janani

[Freesurfer] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST

We are using N4 to correct some large inhomogeneities in some samples and wanted to insert these images into the v6.0 pipeline and bypass the N3 bias correction done within. What would be the correct sequence of freesurfer commands to achieve this? Thanks Eric

Re: [Freesurfer] mris_flatten error: bad vertex

Dear FreeSurfer Experts, Can somebody tell me if there is a solution to this mris_flatten error? I get... MRISreadPatch: bad vertex # (144585) found in patch file and is not about how I save my patch or where. I have done it another 82 times and everything worked perfectly. Any insights/

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Dear Iglesias, We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences). However, we see an artefact similar to the image found in ADNI2 training manual (page 28):

Re: [Freesurfer] Question regarding exporting subcortical segmentation to

Hi Bruce Thanks, mri_binarize works great! Best, Joe Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik Im Neuenheimer Feld 410 69120 Tel.: ++49(0)6221-56-38667

[Freesurfer] V6.1

Dear freesurfer experts, Some days ago I unexpectedly found a thread (about including the flair in the pipeline) in which you mentioned the v6.1. In my lab we are thinking about doing the major 5.1 to 6.0 upgrade, but given that we have a huge database of subjects N~2000) we are wondering