Re: [Freesurfer] Question about coordinates in Freesurfer

External Email - Use Caution I did something similar once. There is a paper on MNI152 to fsaverage conversion options (that suggests a pretty accurate, new method) here: https://www.ncbi.nlm.nih.gov/pubmed/29770530/ If I remember correctly, the simplest way, even though it's not

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfer experts, I want to know how Freesufer to compute the volume and area at each vertex. Are there any references? I just found the reference which introduces the measure of thickness(MacDonald et al.2000). Any help with this would be

[Freesurfer] question for files recon-all generated

External Email - Use Caution Dear expert, I want to know if the *norm.mgz* is already linearly registered？ And is the *T1.mgz *not linearly registered? They are all generated from *recon-all. * Is there any file non-linearly registered? Best wishes, ping ___

[Freesurfer] Fwd: freeview

External Email - Use Caution Have you found any solution? Is it possible to bring my computer to you as a way to solve the problem under your supervision? Thanks a lot. JC. -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 10:50 Subject: freeview

[Freesurfer] Problem while fix topology

External Email - Use Caution Hi Everyone! I have met a problem that when I run the recon-all command, freesurfer always stuck at fix topology and dont give any files modify or terminal return for days. Could you please to help me solve this problem? Thanks!__

Re: [Freesurfer] Question about coordinates in Freesurfer

External Email - Use Caution Dear all, Thank you very much for your kind suggestions. I think it should be mni305. I know how to deal with it now. According to my understanding, the label files transformed from annotations file in the fsaverage should be the mni305 atlas. Then I c

[Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution To whom it may concern I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. Many Thanks! Best Jackie ___

Re: [Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution > To whom it may concern > > I used the freesufer brainstem segmentation, and I want to calculate the > area of the segmented brainstem by slices. Would you like to let me know > the pixel value of all three directions. I used the result in > *brainste

Re: [Freesurfer] (no subject)

Hi Feifei we don't compute thickness using the method introudced by (MacDonald et al.2000). For that you can look at either our 1999 NeuroImage pair of papers or the 2000 PNAS paper. Essentially surface area is just the average area of the triangles that the vertex is attached to, and then v

Re: [Freesurfer] question for files recon-all generated

Hi Ping first, all files in the mri dir are in native coordinates (or "conformed" versions of them), not transformed to any other coordinate system. The norm has been linearly registered to our internal atlas and is subsequently nonlinearly registered to it, but remains in its original coordin

Re: [Freesurfer] Problem while fix topology

that usually means you have a defect that is too large to correct accurately. Can you send us an image of the inflated.nofix surface? Or examine it to see if something went wrong (e.g. skull attached to brain). cheers Bruce On Tue, 16 Jul 2019, Li Ma wrote: External Email - Use Caut

[Freesurfer] 回复： Problem while fix topology

External Email - Use Caution Yep.I have sent through FileDrop to you. -- 发件人：Bruce Fischl 发送时间：2019年7月16日(星期二) 22:19 收件人：Li Ma ; Freesurfer support list 主　题：Re: [Freesurfer] Problem while fix topology that usual

Re: [Freesurfer] optseq2 parameters setup

You are probably interested in the power (ie, "can I detect an effect with this many trials scheduled in this way?"). It is not possible to answer this question without an effect size. Having said that, I generally feel comfortable when the VRF is 20-40. Note that this assumes an FIR (not assum

[Freesurfer] Freeview

External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find

Re: [Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution Dear Jackie, You may want to use the soft segmentations; you can obtain them by setting the environment variable WRITE_POSTERIORS to 1 before running the code, see: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Also: you can obtain t

Re: [Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution Hi, Eugenia I need the real area size of the brainstem in one slice, I can calculate the total pixels in the area from *brainstemSsLabels.v10.mgz*, I need the real pixel size of it, than I can calculate the real area size. Many Thanks! Best Jackie On

[Freesurfer] need for help

External Email - Use Caution Dear Freesurfer, I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec). With the commandlines below i get my inflated surface of MWI map of my patients

Re: [Freesurfer] need for help

Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and pial) On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: External Email - Use Caution Dear

Re: [Freesurfer] Freeview

External Email - Use Caution Hello JC, You can try installing the following,  $ sudo apt-get install qt5-default  qtcreator  $ sudo apt-get install libqt5x11extras5-dev Are you working on Ubuntu 18 ? - R. On Jul 12, 2019, at 22:29, Juan Rivas wrote:Exter

Re: [Freesurfer] Pixel values in Brainstem segmentation {Disarmed}

External Email - Use Caution Hi again, mri_convert will give you the voxel size, which is isotropic. Multiply 2 of the dimensions and you’ve got the area. Also: rather than counting pixels from the discrete segmentation, I highly recommend that you produce soft segmentations as e

[Freesurfer] Fwd: Freeview

External Email - Use Caution Hello, I am working with Ubuntu 18. I did what you asked to me, but the results are the same: *jcrn12@jcrn12-VirtualBox:~$ sudo apt-get install qt5-default qtcreatorReading package lists... DoneBuilding dependency tree Reading state

Re: [Freesurfer] Pixel values in Brainstem segmentation {Disarmed}

mri_info --res file.mgz is probably better than mri_convert On 7/16/19 11:43 AM, Iglesias Gonzalez, Eugenio wrote: > > External Email - Use Caution > > Hi again, > > mri_convert will give you the voxel size, which is isotropic. Multiply > 2 of the dimensions and you’ve got the area. > > A

Re: [Freesurfer] need for help

The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to resp

Re: [Freesurfer] need for help

External Email - Use Caution (I assume now we are discussing in FS list, if no please let me how possible?) Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM analysis over inflated cortex of patients and controls in

Re: [Freesurfer] need for help

On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > (I assume now we are discussing in FS list, if no please let me how > possible?) > > > Thanks Doug, now i could see the inflate surface, this means that my > mri_vol2surf works well. As i would do GLM ana

Re: [Freesurfer] Fwd: Freeview

External Email - Use Caution See if you have the following directory with the plugins libraries, $ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms There should be a libqxcb.so listed in that directory if you have them. Also try setting the following in your environment $ export

Re: [Freesurfer] need for help

External Email - Use Caution Thanks a lot Doug, I started to proceed with FS group analysis wiki you sent to me. Accordingly, i have to resample all my data (output of recon-all for a given subject for example) into fsaverage using mris_preproc. My commandline for a subject was

Re: [Freesurfer] need for help

don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010) On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > Thanks a lot Doug, > > > I started to proceed with FS group analysis wiki you sent to me. > Accordingly, i have to resample all my d

[Freesurfer] Fwd: Fwd: Freeview

External Email - Use Caution That was the systemś answer: jcrn12@jcrn12-VirtualBox:~$ ls /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms libqeglfs.so libqminimalegl.so libqoffscreen.so libqxcb.so libqlinuxfb.so libqminimal.so libqvnc.so jcrn12@jcrn12-VirtualBox:~$ export QT_DEB

Re: [Freesurfer] Fwd: Fwd: Freeview {Disarmed}

External Email - Use Caution OK, please check to see if this directory exists, $ ls /usr/local/freesurfer/bin/platforms If it does exist, then please let us know what is there with a repply email. But I expect that it does not exist and ls will report there is no such platforms d

Re: [Freesurfer] Fwd: Fwd: Freeview {Disarmed}

Hi JC, the following command will attempt to update freeview correctly: bash <(curl -s https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/installers/fv) This is a somewhat experimental script, but hopefully it solves the issue. best, Andrew From: on behalf of fsbuild Reply-To: FS Help

[Freesurfer] DF for Longitudinal LME

External Email - Use Caution Dear Freesurfer Mailing List, I am trying to calculate the effect size of the main and interaction effect clusters that were significant in my vertex-wise LME analysis. For this I need the degrees of freedom for each contrast, but I am confused abou

Re: [Freesurfer] Error in analyze (Qdec)

External Email - Use Caution Hi Greve Can you download those files? I have uploaded it in ftp website and send to your email, the file name is Untitled.rar. Hope you can help me. Thank you very much. Abby Greve, Douglas N.,Ph.D. 于2019年7月15日周一 下午12:07写道： > I see the file there, b