Re: [Freesurfer] Regarding missing DICOM fields

. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics? doug Niels Bergsland wrote: Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM

Re: [Freesurfer] Regarding missing DICOM fields

slice1.dat will be a binary file of the pixel data from the file slice1.dcm. You can do this for each slice, then assemble the data into a real format. Not fun, but possible. Other tools out there might not require the direction cosines. doug Niels Bergsland wrote: Hi Doug, Thanks for the quick

[Freesurfer] Missing Dicom Fields (Revisted)

meant though is if I can manually insert the values using, for example, dcmodify (part of the DCMTK) and then process the scans with Freesurfer. Hopefully this is a bit more clear! Thanks again, Niels Bergsland ___ Freesurfer mailing list Freesurfer

[Freesurfer] Re: Missing Dicom Fields (Revisted)

anything about. doug Niels Bergsland wrote: Hi again, From the last time that I asked about this, the project was temporarily put on hold, but now it has started up again... When looking back at the responses from last time, I realized that I am not sure if I made it clear what I

[Freesurfer] mri_convert on 64bit vs 32bit

the 64 bit install extensively before and never run into this issue. Any insight? Thanks! Regards, Niels Bergsland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_convert on 64bit vs 32bit

the 32bit and 64bit builds though. I have not personally encountered the message you are seeing. Nick On Thu, 2006-10-12 at 16:40 -0400, Niels Bergsland wrote: Hi, I am experiencing quite a strange problem. I have a set of DICOMs that when I run the following on a 32bit machine, it works fine

[Freesurfer] White matter and pial surfaces not tracking sulcus

Hi all, I have run into an issue that I am having trouble correcting. http://imgur.com/a/4KqpJ I have checked the aseg to see if it was labeled as ventricle. This does not seem to be the cause. Any other suggestions? I am happy to upload the case if that is necessary. Best regards, Niels

Re: [Freesurfer] White matter and pial surfaces not tracking sulcus

Hi all, Sorry for the repost, was just wondering whether someone might have some input regarding this issue. Thanks! Niels On Thu, Mar 26, 2015 at 12:10 PM, Niels Bergsland theni...@gmail.com wrote: Hi all, I have run into an issue that I am having trouble correcting. http://imgur.com

Re: [Freesurfer] report a bug

Hi - sounds like it's running out of memory and getting killed. How much RAM do you have? On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea...@libero.it < salvatoreandrea...@libero.it> wrote: > Hi! > - I am using Ubuntu 14.4 (trusty). > > - This is my subject directory:

Re: [Freesurfer] recon-all base error

Hi - how much memory do you have on your machine? On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea...@libero.it < salvatoreandrea...@libero.it> wrote: > Hi Freesurfer experts! > > I tried to run recon-all base for a longitudinal analysis on my data. But > I get the following error: > > > >

Re: [Freesurfer] R: Re: report a bug

Hi - that's way too low, unfortunately. You need at least 4GB and more is preferred. See: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements On Mon, Nov 30, 2015 at 5:19 PM, salvatoreandrea...@libero.it < salvatoreandrea...@libero.it> wrote: > I have around 2 Gb of total RAM. Isn't

Re: [Freesurfer] Difficulties running tracula

Hi Anastasia and John, This looks like the glibc issue that was fixed in more recent versions of FSL. Given that you are running Ubuntu 16.04, if you are using an older version of FSL, you will get FLIRT matrices saved in hexadecimal format. If you upgrade your FSL to a more recent version, you

Re: [Freesurfer] Difficulties running tracula

Hi again, The latest version is 5.0.10 but the issue was definitely fixed in 5.0.9 (possibly one point release earlier, I can't recall). Regardless, I don't think there were any changes to flirt between 5.0.9 and 5.0.10. Good luck! Niels On Fri, Feb 16, 2018 at 5:40 PM, John Davis

Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

External Email - Use Caution Hi all, Not sure if this was resolved off-list or not, but I just ran into it myself and it turned out to be a permissions-related error in that the user didn't have read access to some of the required files in the Matlab runtime. Setting them

Re: [Freesurfer] mri_segment error

Your input here is a localizer image: Protocol t2_haste_localizer_p2 On Mon, Mar 19, 2018 at 12:51 PM, Z Hessam wrote: > > hello, i have problem again with a new data set. > this is the recon-all.log file in attach > > thanks a lot > > > On Fri, Feb 9, 2018 at

[Freesurfer] Longitudinal brainstem structures / thalamic nuclei

External Email - Use Caution Hi Eugenio, Just wanted to ask quickly if there is plan to implement longitudinal processing for the brainstem structures and thalamic nuclei modules? Thanks! Niels ___ Freesurfer mailing list

Re: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei

ugenio Iglesias > > Centre for Medical Image Computing (CMIC) > > Department of Medical Physics and Biomedical Engineering > > University College London > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of Niels > Bergsland > *Re

[Freesurfer] Disjointed thalamic nuclei segmentation

External Email - Use Caution Hi Eugenio, Thank you again for the fantastic thalamic nuclei segmentation tool! I'm going through and QC'ing a batch of subjects that were processed through the pipeline. Data was originally processed with freesurfer-6.0.0 and then processed through

Re: [Freesurfer] e-TIV

External Email - Use Caution Hi, This won't affect the eTIV as that is derived purely from the affine registration. See Buckner et al. (2004) NeuroImage 23:724-738. for more details. -Niels On Mon, Nov 26, 2018 at 6:46 AM 박경일 wrote: > External Email - Use Caution > >

Re: [Freesurfer] Minimum FS version for thalamic segmentation

-- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Niels Bergsland < > theni...@gmail.com> > *Sent:* Wednesday, September 12, 2018 1:25:18 PM > *To:* Freesurfer Mailing List > *Subject:* [Freesurfer] Minimum

[Freesurfer] Minimum FS version for thalamic segmentation

External Email - Use Caution Hi Eugenio, Just a quick question - is there a minimum version of FS that is required to run the thalamic nuclei segmentation? I am just thinking about some old datasets that we have that were run with FS 5.1. Thanks and best wishes, Niels

Re: [Freesurfer] Error with "recon-all -make all" following multiple manual editing

External Email - Use Caution Hi all, Just following up on this as I've run into the exact same problem. Is there a different recon-all.makefile that should be used for FS 6/6.0.1 ? Thanks! On Fri, Mar 29, 2019 at 9:28 AM Matthieu VANHOUTTE < matthieuvanhou...@gmail.com> wrote: