[Freesurfer] pass code for FreeSurfer virtual machine

External Email - Use Caution Dear Freesurfer help team This is Rana Ghamari and I have just downloaded Ubuntu compressed image with the FreeSurfer. Would you mind giving me a pass code to open the zipped file? Best regards Rana ___ Free

[Freesurfer] sending email to post to FreeSurfer mailing list

External Email - Use Caution ghamarir...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to w

Re: [Freesurfer] aseg stats meaning

External Email - Use Caution Does anyone know what the column headings: normMean normStdDev normMin normMax normRange are telling us? On Tue, Jun 20, 2023 at 3:23 PM Michael Mc Laughlin wrote: > That solves the Supratentorial volume question, but it doesn't > explain the nor

Re: [Freesurfer] Use synthetic in recon-all pipeline

External Email - Use Caution Thank you, Douglas and Malte! In terms of mask volume, synthstrip and watershed method in FS7.3.2 gave us very similar results. But synthstrip takes better care of dura in our case. Best, Ruideng On Wed, Jun 21, 2023, 1:00 PM Hoffmann, Malte,PhD wro

[Freesurfer] Obliqueness in the input images for recon-all

External Email - Use Caution Dear all, We acquired the images (sagittal, 176*256*256) with obliqueness, because we tried to match the prescription with the subject's head positioning. Then, the obliqueness is shown in the header of the image. We used this image in recon-all. Afte

Re: [Freesurfer] Freesurfer binary for Centos 9

External Email - Use Caution I would suggest someone try installing the CentOS8 RPM file and if that succeeds, then you could try running freesurfer.   However, freesurfer has not been tested running on “CentOS9 stream” or the current RHEL 9 release and I would not expect it to

[Freesurfer] Vbox password

External Email - Use Caution Would you please send me the unzip pass for freesurfer again? The last one did not work___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer T

Re: [Freesurfer] Use synthetic in recon-all pipeline

External Email - Use Caution Hi Ruifeng, While we intend to replace the skull-stripping in recon-all with SynthStrip in the long run, I think this is not fully implemented yet, I'm afraid. In general, the --no-csf flag would be recommended as this produces a skull strip similar

Re: [Freesurfer] Pial and White surface maps are not found

External Email - Use Caution p.s. I am wondering whether this specific issue arises while working with freesurfer using Linux based Virtual Machine? On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran wrote: > Hi Yujing > > Thank you very much for your quick reply. Yes, I used a dir

Re: [Freesurfer] Pial and White surface maps are not found

External Email - Use Caution Hi Varun, I’m not sure what issue that you have been running into. Can you send your recon-all.log? In general, you need to 1. set environment variable SUBJECTS_DIR to some directory that you have write permission 2. pass full path to T1 image to -i

[Freesurfer] Pial and White surface maps are not found

External Email - Use Caution Hi FS experts, It's been a few years, I used FS tools for cortical surface reconstruction. Now, when I used the freesurfer 7.2 version to perform cortical surface reconstruction on the T1-weighted structural MRI data, I was unable to obtain the lh/rh.p

[Freesurfer] Inconsistent number of ROIs in ?.aparc.DKTatlas.stats

External Email - Use Caution Hello, I am running into a major issue when I run recon-all -all on the OASIS1 cohort. I am getting an inconsistent number of ROIs for the same subject between the lh and rh, resulting in different sizes of connectivity matrices across subjects (var

[Freesurfer] Inconsistent number of ROIs in ?.aparc.DKTatlas.stats

External Email - Use Caution Hello, I hope my email finds you well. I am running into a major issue when I run recon-all -all on the OASIS1 cohort. I am getting an inconsistent number of ROIs for the same subject between the lh and rh, resulting in different sizes of connectivi

[Freesurfer] request for password

External Email - Use Caution Dear freesurfer, I'm a medical physics student at the University of Manchester, I just downloaded the FS_7_2_0_ubuntu_18_04_06.ova.7z on my mac computer. please send me a password. Best, Yifei ___ Freesur

[Freesurfer] Pass code Request

External Email - Use Caution Hello, I am installing Freesurfer on a Windows 10 device and I have been asked for a passcode to open the 7z file. Please can I request this? Thank you, Freya ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] Freesurfer binary for Centos 9

External Email - Use Caution Dear Freesurfer surfer experts, Will Freesurfer surfer be built for Centos 9 as the cluster I am using has now been upgraded to Centos 9? Is there a source package for Freesurfer 7.4.1? Best regards, Knut Jørgen Bjuland __