Re: [Freesurfer] Showing graph of freesurfer atlas

why don't you use the inflated surface instead? On Wed, 23 Jan 2019, charujing123 wrote: External Email - Use Caution Hi FS experts and users I am interested in the ROI (e.g., superiorfrontal) location on the surface. Now I only can perform this ,but this method is

[Freesurfer] Showing graph of freesurfer atlas

External Email - Use Caution Hi FS experts and users I am interested in the ROI (e.g., superiorfrontal) location on the surface. Now I only can perform this ,but this method is difficult to detect the superiorfontal region. " freeview -v \ bert/mri/T1.mgz \

[Freesurfer] Fwd: updateing freesurfer.

External Email - Use Caution Same here. Any help with this issue? SIP is off! Thanks Joe -- Forwarded message - From: Aaron Tanenbaum Date: Tue, Oct 16, 2018 at 11:16 AM Subject: [Freesurfer] updateing freesurfer. To: Freesurfer External Email - Use

[Freesurfer] "slides" link is not working

External Email - Use Caution https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Error Message: Not Found The requested URL /pub/docs/freesurfer.groupanalysis.short.pdf was not found on this server. ___ Freesurfer mailing list

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

Can you send the full terminal output and/or the log file? On 1/22/19 2:53 PM, Amrita Bedi wrote: > > External Email - Use Caution > > Hello Freesurfer developers, > > I was following the functional connectivity walkthrough for resting > stage BOLD data and I got the attached error when

Re: [Freesurfer] Version 6.1 and aseg histograms

On 1/22/19 2:59 PM, Hatton, Sean wrote: > External Email - Use Caution > > Hi all, > > Two quick questions: > > 1. Is there an expected timeframe for when FreeSurfer 6.1 (or next version) > is published? Not a firm date. We have started the process to release a new version. Last

[Freesurfer] nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)

External Email - Use Caution Dear freesurfer team, I have been having a problem running freesurfer on one computer. The same commands and data work fine on other machines. The error message is: nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)

[Freesurfer] LME MATHLAB tools

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use

[Freesurfer] test

External Email - Use Caution This is a test ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Version 6.1 and aseg histograms

External Email - Use Caution Hi all, Two quick questions: 1. Is there an expected timeframe for when FreeSurfer 6.1 (or next version) is published? 2. In aseg, is there a way to manually select the histograms or mean/SD of the ROIs? Regards, Sean Hatton, PhD Assistant

[Freesurfer] LME MATLAB tools

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model

[Freesurfer] Functional connectivty walkthrough step 8 error

External Email - Use Caution Hello Freesurfer developers, I was following the functional connectivity walkthrough for resting stage BOLD data and I got the attached error when I ran step 8 (selxavg3-sess). Does anyone have any thoughts on how to trouble shoot this? Not sure if

Re: [Freesurfer] Error in running make_average_subject

This has been fixed in our development version. I can give you a new script or you can try this: cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI! ln -s orig.mgz norm.mgz Then re-run make_average_subject * On 12/14/18 1:43 PM, Emanuel Alvaredo wrote: > > External Email - Use Caution > >

Re: [Freesurfer] mapping a volumetric statistical map to the cerebellum surface

Is grf.th1.3.pos.sig.cluster.mgh in the mni152 2mm space? You should check the registration with tkregister2 --mov grf.th1.3.pos.sig.cluster.mgh --reg $FREESURFER_HOME/average/mni152.register.dat --surfs It looks like you projected it to the white surface of fsaverage On 1/22/19 2:08 PM, john

Re: [Freesurfer] mapping a volumetric statistical map to the cerebellum surface

External Email - Use Caution Hi Dr Greve, Thanks for the comment: I ran vertex wise analysis on subcortical regions, I corrected the analysis for multiple comparison using "mri_glmfit-sim". One of the created files after correction for multiple comparison is

Re: [Freesurfer] fsaverage, brainstem and cerebellum

You are going about it in the right way. Not sure about a better template. You could create the surfaces on an individual and then apply a linear transform to get it into fsaverage space. Again, another hack ... On 1/22/19 1:56 PM, john Anderson wrote: > External Email - Use Caution >

Re: [Freesurfer] mapping a volumetric statistical map to the cerebellum surface

Can you be more specific about how mri_vol2surf failed? Eg, command line, terminal output, reason you think it did not work On 1/21/19 10:47 AM, john Anderson wrote: > > External Email - Use Caution > > Dear FS experts, > I have a statistical map from the output of a surface based

Re: [Freesurfer] FSFAST poor registration

Are you saying that all of them have bad registrations? Some of them (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101) look like they could be bad. For the bad ones, are you totally sure that the subjetname file has the correct name of the subject? On 1/21/19 3:19 AM, Keri

[Freesurfer] Problems with GM segmentation

External Email - Use Caution Dear Free Surfer team, I few days ago I sent you personally the dicom files as well as the mask of the lesion you asked me for as I am having problems with GM segmentation. I would greatly appreciate if you could help me with this issue and tell me

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Hi Dr Greve, thank you for the response... It is a genius hack ;-) Results are way much better. My objective is just to improve visualization... I would like to project statistical maps from vertex wise analysis of subcortical regions. The same last

Re: [Freesurfer] mri_segstat: same output with two different label

I don't know what is happening. If the two z-maps are really different, then it should have given different values. Run this mri_diff order/z.nii.gz disorder/z.nii.gz Does it indicate that there is a difference? If so, can you run your two mri_segment commands and send me the terminal output of

Re: [Freesurfer] problems with bbregister's output image

You have effectively applied the registration twice, once when you ran bbregister to get the output and once when you ran tkregister2 with --reg. Try that tkrister2 command with func.nii.gz as the --mov On 1/21/19 6:35 PM, Sam W. wrote: > > External Email - Use Caution > > Hello, > > I

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

Use gr...@nmr.mgh.harvard.edu On 1/22/19 1:19 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug > > Thanks for the link but it won't let me transfer the file. I tried FileDrop > but it requires an nmr.mgh.harvard.edu account and told me that user

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

External Email - Use Caution Hi Doug Thanks for the link but it won't let me transfer the file. I tried FileDrop but it requires an nmr.mgh.harvard.edu account and told me that user dgreve is not valid. Sorry for the hassle. François On 1/22/19, 1:00 PM, "Greve, Douglas

Re: [Freesurfer] Error using mri_convert and recon-all {Disarmed}

glad to hear it worked out Bruce On Tue, 22 Jan 2019, Isil Bilgin wrote: External Email - Use Caution Dear both,  thank you so much for your help and recommendations. I talked to our IT and they gave me all the necessary permissions, so everything seems working now.  Thank

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

Not sure. Can you tar up the subject and send me the file here  ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it is transferred. On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan

Re: [Freesurfer] Error using mri_convert and recon-all {Disarmed}

External Email - Use Caution Dear both, thank you so much for your help and recommendations. I talked to our IT and they gave me all the necessary permissions, so everything seems working now. Thank you very much indeed, Kind regards Isil On Tue, Jan 22, 2019 at 4:52 PM

Re: [Freesurfer] fsaverage, brainstem and cerebellum

You can try mri_binarize with both --erode and --dilate (specifying the structures with --match and and output surface with --surf). Dilating then eroding might remove some of the holes (though it is a hack) On 1/22/19 10:43 AM, Bruce Fischl wrote: > Hi John > > sorry, not really. If you

Re: [Freesurfer] Clinical Scan Thickness

Not for cortical analysis. You might be able to get something useful from subcortical analysis On 1/22/19 12:15 PM, Sahnoune,Iman wrote: > > External Email - Use Caution > > Hello, > > I’m writing to ask whether clinical scans with thickness of 5mm are > currently able to be analyzed

Re: [Freesurfer] Calculating global thickness

Personally, I think it is fine just to do the average On 1/11/19 5:00 PM, Arsenije Subotic wrote: > > External Email - Use Caution > > Dear experts, > > > When calculating global thickness, is it fine to simply use an average > of lh.thickness and rh.thickness, or is it necessary to

Re: [Freesurfer] Average of surfaces

tru mri_concat lh.PET.subject1.nii,gz h.PET.subject2.nii,gz lh.PET.subject3.nii,gz  lh.PET.subjectN.nii,gz --mean --o lh.PET.mean.nii.gz On 1/11/19 10:37 AM, john Anderson wrote: > > External Email - Use Caution > > Dear FS experts, > I resampled PET images for multiple subjects I

[Freesurfer] Clinical Scan Thickness

External Email - Use Caution Hello, I’m writing to ask whether clinical scans with thickness of 5mm are currently able to be analyzed using Freesurfer? This question has been asked in the archives, but it has been about 5 years so just writing to see whether that has changed

Re: [Freesurfer] Surface maps of cortical thickness

Use mri_concat avg-lh-thickness.15.mgh --std --o avg-lh-thickness.15.std.mgh You can compute mean with --mean instead of --std On 1/9/19 9:19 AM, Schranzer René wrote: > > External Email - Use Caution > > Hello everyone, > > I have some problems with the computation of the SD of

Re: [Freesurfer] Error using mri_convert and recon-all

Hi Isil, this issue might resolve itself once the executable permissions are taken care of, but if not, it's possible it's related to the dicom input. If you're still getting the error, can you run recon-all with the -debug flag and send us the output? best, Andrew On 1/22/19, 11:23 AM,

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Thanks, Yixin. It just ran to completion on my machine with FreeSurfer 6.0. Let me know if you want me to send you the output. Did you notice this problem on other subjects? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre

Re: [Freesurfer] Error using mri_convert and recon-all

Hi Isil I'll leave it to someone else to answer the first quesion, but if mri_convert is not executable I can't understand how recon-all can run at all, so you should probably get someone with root access to fix that first cheers Bruce On Sat, 19 Jan 2019, Isil Bilgin wrote:

Re: [Freesurfer] bug repport freeview crash with symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference

Hi, we've recently modified the freeview update instructions (at https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview) to hopefully account for this. Can you give those a try and let me know how it goes? thanks, Andrew On 1/22/19, 5:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] Highlighting single atlas structures in freeview

Hi Francesco, the linux dev distributions are built on 64bit centos6 and 7, so you’re right about your original issue being related to the 32bit vm. I think your newer Qt errors are related to out-of-date libraries supplied in the ‘Update Freeview’ instructions. I’ve just updated that wiki page

Re: [Freesurfer] DKT40 classifier atlas

Hi Yixin not sure what you mean by "reconstruct", but we do distribute the atlas. The files can be found in $FREESURFER_HOME/average/*DKT*.gcs, although I don't think we have documented the details of the .gcs file format (it holds a bunch of information including spatial priors and priors

Re: [Freesurfer] fsaverage, brainstem and cerebellum

Hi John sorry, not really. If you constrain the topology of the cerebellum you will probably loose a lot of it since the folia are so small. You can try using Florent Segonne's old code (mri_topologycorrection), which will generate a discrete segmentation that has the correct topology

Re: [Freesurfer] ?????? how to register feature maps to fsaverage6?

can we take a step back. What feature maps are you trying to map? recon-all will create individual subject thickness maps by default (lh.thickness/rh.thickness) and will also map them to fsaverage if you specify -qcache. If you want to further map those to fsaverage6 you should use

[Freesurfer] DKT40 classifier atlas

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask how can I reconstruct the DKT40 classifier atlas. Is it included in recon -all? Thank you for your help. Best regards, Yixin Ma ___ Freesurfer mailing list

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Hi Dr. 00246.zip Iglesias I have the problem of hippocampus subfield division not working. You mentioned that I can upload one of the subjects as an example. I'm

Re: [Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates

External Email - Use Caution Thanks for getting back so quickly, Anastasia. I assume you are answering a question about what dmri_trk2trk is doing. Could you please confirm? Could you also please look at the sequence of transforms I am using and confirm that these are correct?

Re: [Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates

Hi Donald - Both your input and output reference volume are in diffusion space and there is no transformation specified, so the output is also in diffusion space. These are voxel, not RAS, coordinates. Best, a.y On Jan 22, 2019 7:14 AM, "Krieger, Donald N." wrote: External Email -

[Freesurfer] Using PetSurfer to derive R1 values from early-phase dynamic PET

External Email - Use Caution Hello Doug and PetSurfers, I would like to extract relative regional cerebral blood flow (R1) data from early time-interval of dynamic PET data (i.e. 11C-PiB) using the MRTM2 technique in PetSurfer. The time interval that I am interested in is

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Hi Dr Bruce, I applied your recommendations and I was able to create surfaces to the cerebellum and brain stem using the command mri_tesselate. I am not happy with the topology though... There are holes and some defects. Would you recommend any

[Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates

External Email - Use Caution I extract the streamlines for each tract from path.pd.trk to an ascii file and then wish to transform the coordinates to RAS T1 coordinates in millimeters. My results are not correct. Here is the extraction command I'm using. Is this correct? Perhaps

[Freesurfer] bug repport freeview crash with symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference

External Email - Use Caution I have update to the latest freeview, when I start I got this error message. Copyright (C) 2018 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change

Re: [Freesurfer] Highlighting single atlas structures in freeview

External Email - Use Caution As per an older thread , this might be in fact due to the VM being 32bit. It is mentioned there the 64bit VirtualBox image is widely available, but I on the main FS

Re: [Freesurfer] Highlighting single atlas structures in freeview

External Email - Use Caution Hi Ruopeng, Thanks! I took those steps to update Freeview, but when I try to start (the updated) Freeview, the command line returns "bash: /usr/local/freesurfer/bin/freeview: cannot execute binary file". Maybe there is something wrong in the update