Re: [Freesurfer] Recon-all with/without T2 give the same stats

External Email - Use Caution Hi Dr. Greve, I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses (and the other measures like volume and area) are all the same. Thanks, Jianzhong Greve, Douglas N.,Ph.D. 于2018年10月9日周二 上午10:16写道： > The aseg.stats should be the same si

Re: [Freesurfer] Recon-all with/without T2 give the same stats

The aseg.stats should be the same since that does not make reference to the surfaces. The aparc stats should have been different because the thickness should have been different. Can you check whether the thickness files are different? On 10/8/18 9:39 AM, Jianzhong Chen wrote: External

Re: [Freesurfer] Mri Convert Help

Sorry, there are a lot of things going on down there, it is hard to figure out what is happening. It looks like the sourcing of SetUpFreeSurfer.sh is failing is that right? Then it looks like the copy (cp) is failing. Then when you run mri_convert, it looks like another bash error. It looks like

[Freesurfer] Mri Convert Help

External Email - Use Caution Hello Everyone, I hope you are doing well! I am trying to recon-all a DICOM file, for the ultimate hope of being able to identify the location of M1 via parcellation. I have successfully been able to do so for 2 subjects already, though for some reason

Re: [Freesurfer] FW: RE: error glm-fit-sim

were there any clusters that survived? On 10/8/18 12:12 PM, Caroline Beelen wrote: External Email - Use Caution The command: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_thresh

[Freesurfer] Talairach failed in monkey brain

External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey brain, i encountered an error during talairach registration step, i have used tkregister2 to manually edit the registration but i have gotten error there too: tkregister2 --targ /usr/local/fr

Re: [Freesurfer] Difference between 6.0.1 and 6.0.0

Hello Haakon, I don’t there are significant functionality changes in the 6.0.1 patch release. i think there are however changes to fix some run time errors with respect to system libraries found/used on the system running Freesurfer. Someone else who mentors the help list might chime in, but

Re: [Freesurfer] hippocampal subfields

External Email - Use Caution Thanks, Marcel. Can you please send us the whole output (can be found in the log file) Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://

[Freesurfer] hippocampal subfields

External Email - Use Caution Dear Eugenio, there is one error in the error.log: 'Could not set locale'. Best regards Marcel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

External Email - Use Caution Glad to hear. As much as it exists to solve problems, it’s also nice to get positive news on the list every once in a while. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College Lo

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

External Email - Use Caution Hi Iglesias, It turns out that my input images are in different orientation and I had a hard time reorienting them. Starting from dicom images and using mri_convert to bring them to nifti format seem to fix the problem The hippocampal subfiled segmenta

Re: [Freesurfer] output values of vertices on surface into a textfile

External Email - Use Caution Thanks so much! Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu On 10/8/18, 11:30 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: Hi Sar

Re: [Freesurfer] output values of vertices on surface into a textfile

Hi Sara something like: mris_convert -c lh.your_overlay lh.white lh.your_overlay.asc should do the trick cheers Bruce On Mon, 8 Oct 2018, Sims, Sara A wrote: External Email - Use Caution Doug, I'm sorry. It is actually a surface overlay. So same question but about overlays: How

Re: [Freesurfer] output values of vertices on surface into a textfile

External Email - Use Caution Doug, I'm sorry. It is actually a surface overlay. So same question but about overlays: How could I output the location and value information? Sara Sims On 10/3/18, 12:10 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,

[Freesurfer] FW: RE: error glm-fit-sim

External Email - Use Caution The command: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -view

Re: [Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

Hi Maedeh what does the annotation file LDestrieux200 look like? If you apply it to the subject test1 does it work? if you want to send us that subject dir and the lh.LDestrieux200.annot and lh.Destrieux200.gcs files we will take a look cheers Bruce p.s. sorry for missing your email the fir

[Freesurfer] Difference between 6.0.1 and 6.0.0

External Email - Use Caution Dear Experts. I just happened to stumble across version 6.0.1, what is the main difference from 6.0.0? And I read in a post from 2017 that the flairpial wasn't optimized in v6.0.0 compared to 5.3, and that this would be optimized in version 6.1. Any

[Freesurfer] Recon-all with/without T2 give the same stats

External Email - Use Caution Dear All, I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the aseg stats and aparc stats with/without T2 are exactly the same. When I check the pial surfaces, I can see that they are very similar but not the same. So is it rea

Re: [Freesurfer] Hippocampal/Amygdala subfield segmentation error - Freesurfer devel-20180612

External Email - Use Caution Hi Sally, It is indeed the linear registration used to initialize the atlas deformation that is going crazy. Do you think you could upload the subject, so we can take a look? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre

[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

External Email - Use Caution Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as