Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

fer-boun...@nmr.mgh.harvard.edu > On Behalf Of KennethSPrice > Sent: Sunday, September 17, 2023 11:35 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) > synthsr scan > > External Email - Use Caution > > I'

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html Hope this helps. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of KennethSPrice Sent: Sunday, September 17, 2023 11:35 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

External Email - Use Caution I've set the coredumpsize to unlimited, and still get the same error. Could it be something with the installation? build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

External Email - Use Caution Hello Ken, The output from your linux shell limits in the log show the following, cputime      unlimitedfilesize     unlimiteddatasize     unlimitedstacksize    8192 kbytescoredumpsize 0 kbytesmemoryuse    unlimitedvmemoryuse   unlimiteddescriptors 

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

External Email - Use Caution OK, I've attached the log file. --- Original Message --- On Friday, September 15th, 2023 at 2:59 PM, fsbuild wrote: > External Email - Use Caution > > It might help if you could send along the crash report as an attachment.. > > -R. > >> On S

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

External Email - Use Caution  It might help if you could send along the crash report as an attachment. -R. On Sep 15, 2023, at 14:36, KennethSPrice wrote:External Email - Use CautionUpdate: I tried running recon-all (5.1, ubuntu 18

Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

External Email - Use Caution Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated. Thanks, K --- Original Message --- On Thursday

[Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

External Email - Use Caution Howdy yall, I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mr

Re: [Freesurfer] mri_convert --conform

Giuseppe Sent: Monday, April 24, 2023 12:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert --conform External Email - Use Caution Hello, Could you please tell me which formula is used by the command "mri_convert --conform" to rescale the input image t

[Freesurfer] mri_convert --conform

External Email - Use Caution Hello, Could you please tell me which formula is used by the command "mri_convert --conform" to rescale the input image to 0-255. I could not find it. Thank you, Giuseppe ___ Freesurfer mailing list Freesurf

Re: [Freesurfer] mri_convert mosaic dicoms

it might be. That override was for a particular experimental case, but if it works, it works On 3/27/2023 2:06 PM, John Anderson wrote: External Email - Use Caution Thank you, Dr Greve.  I tried it, but it didn't work. By 'didn't work,' I mean that when I visualized the NIfTI file, I

Re: [Freesurfer] mri_convert mosaic dicoms

External Email - Use Caution Thank you, Dr Greve. I tried it, but it didn't work. By 'didn't work,' I mean that when I visualized the NIfTI file, I saw a line on the coronal and sagittal planes, and the whole brain on the axial view. I was able to generate a NIfTI image with multi

Re: [Freesurfer] mri_convert mosaic dicoms

Can you try it with --dcm2niix ? On 3/25/2023 9:43 AM, John Anderson wrote: External Email - Use Caution Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert

[Freesurfer] mri_convert mosaic dicoms

External Email - Use Caution Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails

Re: [Freesurfer] mri_convert mosaic data

Behalf Of John Anderson Sent: Thursday, March 23, 2023 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_convert mosaic data External Email - Use Caution Thank you. I would appreciate feedback from developers on two issues. 1) mri_convert in FS v6 is unable to convert any

Re: [Freesurfer] mri_convert mosaic data

rt those DICOMs? It will use dcm2niix to > convert. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *John Anderson > *Sent:* Wednesday, March 15, 2023

Re: [Freesurfer] mri_convert mosaic data

Behalf Of John Anderson Sent: Wednesday, March 15, 2023 1:46 PM To: Freesurfer support list Subject: [Freesurfer] mri_convert mosaic data External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files

[Freesurfer] mri_convert mosaic data

External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D

Re: [Freesurfer] Freesurfer mri_convert

please send the command line, log file, version of FS, etc On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote: External Email - Use Caution Dear FS Experts I am having continued issues with the mri_normalize function on MPRAGE data I get an error message: 3d normalization pass 1 of 2 e

[Freesurfer] Freesurfer mri_convert

External Email - Use Caution Dear FS Experts I am having continued issues with the mri_normalize function on MPRAGE data I get an error message: 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points err

Re: [Freesurfer] mri_convert help w/ GE Genesis files

Have you tried dcm2niix? It's pretty robust On 6/17/2021 6:59 PM, Christopher Mcnorgan wrote: External Email - Use Caution External Email - Use Caution Hi all, I’ve been provided with some data collected on a 1.5T GE scanner from an old published study. The paper doesn’t ind

[Freesurfer] mri_convert help w/ GE Genesis files

External Email - Use Caution Hi all, I’ve been provided with some data collected on a 1.5T GE scanner from an old published study. The paper doesn’t indicate the scanner model (beyond that it’s a 1.5 GE scanner), but I believe they came from a GE Genesis, based on the .MR file e

Re: [Freesurfer] mri_convert error for creating flat_lh.gii file

Try adding a -p as below (-p indicates that it is a patch) mris_convert -p lh.full.flat.patch.3d flat_lh.gii On 4/20/2021 2:50 PM, Suzanne Nie wrote: External Email - Use Caution Hello Freesurfer Developers, I'm attempting to create a full surfaces folder in the filestore based on t

Re: [Freesurfer] mri_convert problem

, 2021 at 11:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert problem External Email - Use Caution Dear List, I have installed the ubuntu version of freesurfer (creating the VM as in the tutorial) I would like to run the following command: mri_convert -c -oc 0 0 0

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

External Email - Use Caution Yes, it runs to completion with --no-dwi. And for now, we don't need the bvals and bvects. Thanks a lot for your help! On 26.01.2021 16:16, Douglas N. Greve wrote: > It throws an error when trying to extract the bvals or bvects. Can you try it >

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

It throws an error when trying to extract the bvals or bvects. Can you try it with --no-dwi and see if it runs to completion? If it does, do you have another way to get the bvals and bvects? On 1/26/2021 3:33 AM, Hannah Eichhorn wrote: External Email - Use Caution Thanks for your ans

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

External Email - Use Caution Thanks for your answer! The full command line is: mri_convert /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

Can you send the full command line and terminal output? On 1/22/2021 4:29 AM, Hannah Eichhorn wrote: External Email - Use Caution ​Dear all, I am trying to convert Dicom volumes from a DWI Siemens sequence into nifty format, but I get the following error when I run the mri_convert T

[Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

External Email - Use Caution ​Dear all, I am trying to convert Dicom volumes from a DWI Siemens sequence into nifty format, but I get the following error when I run the mri_convert Test.IMA Test.nii command: ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7  DICOM Fi

Re: [Freesurfer] mri_convert error

It looks like it is trying to extract diffusion info. Try running it with --no-dwi On 11/2/2020 5:11 PM, Georgina Angelopoulou wrote: External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files t

[Freesurfer] mri_convert error

External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me

[Freesurfer] mri_convert error

External Email - Use Caution Dear Freesurfer Developers, Apologies for double posting. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me to resolve the pro

Re: [Freesurfer] mri_convert input files

Sorry, we can't convert PAR/REC files. On 4/8/2020 4:20 AM, Setiaman, N. wrote: External Email - Use Caution Hi, I would like to convert my raw scans to nifty. The scans are made on a Philips scanner. I was able to retrieve most of them as DICOM files, but some of them are only avai

[Freesurfer] mri_convert input files

External Email - Use Caution Hi, I would like to convert my raw scans to nifty. The scans are made on a Philips scanner. I was able to retrieve most of them as DICOM files, but some of them are only available as PAR/REC. Does mri_convert also handle PAR/REC or can I only conver

Re: [Freesurfer] mri_convert no scaling

output saying it is not rescaling cheers Bruce On Wed, 9 Oct 2019, Ezequiel Mikulan wrote: External Email - Use Caution Dear All,  I have a similar problem to the one posted here ( Re: [Freesurfer] mri_convert scaling ). In my case I'm trying to convert from ANALYZE

[Freesurfer] mri_convert no scaling

External Email - Use Caution Dear All,  I have a similar problem to the one posted here ( Re: [Freesurfer] mri_convert scaling ). In my case I'm trying to convert from ANALYZE (.img, .hdr and .mat) to NIFTI and I need to keep the scale as in the original file. I've

Re: [Freesurfer] mri_convert for Philips dicoms

Try dcm2niix (not part of FS, you'll have to download and install) On 9/17/19 3:10 PM, Mun, Anna wrote: > Dear FreeSurfer team, > > I am working with data sent to us from other research site. They use > Philips scanner and I can not run mri_convert on the dicoms. Is there > other way to mri_conv

[Freesurfer] mri_convert for Philips dicoms

Dear FreeSurfer team, I am working with data sent to us from other research site. They use Philips scanner and I can not run mri_convert on the dicoms. Is there other way to mri_convert and reconstruct Philips dicoms. error log is: WARNING: tag SeriesNumber not found WARNING: tag image orientat

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution Hello Caspar, So are you saying that if you run directly from the terminal in bash (or maybe in csh with % sign as prompt) $ mri_convert -i inputvolume.mgz --out_orientation LPS -iis .5 -ijs .5 -iks .5 -vs 1.2 1.2 1.2 - that the command works, but it

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution Hi! Unfortunately, it turns out that downgrading glibc does not solve this issue, neither with .14 nor with .15 versions. Doug, we are calling mri_convert from a csh script, with the following options: mri_convert -i inputvolume.mgz \ -o outputvolume.n

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

Can you send the command line and full terminal output? On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > > Hi! > We are getting segmentation fault (core dumped) error when trying to > run mri_convert on NIFTI files. This is running Freesurfer v5.3 on >

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution ​Hello Caspar, So far, I have not found a CentOS rpm with that 2.14 version of libcrypt, but you can download the source from the GNU project and try building it on your machine with the following steps. - R. 1) Become root in your terminal window an

Re: [Freesurfer] mri_convert issues

rent computers. I don't know which is > the error, any more ideas? > > Best, > Jennifer > > > De: freesurfer-boun...@nmr.mgh.harvard.edu > en nombre de Tim Schäfer > > Enviado: jueves, 16 de mayo de 2019 11:50 > Para: Free

Re: [Freesurfer] mri_convert issues

Hi Jennifer try mri_convert -it nifti1 input.img output.nii.gz you might not need the "-it nifti1" are you sure it's a nifti and not analyze? You need to be careful you have the correct direction cosines to make sure you know which is left and which is right. Definitely bring it up in free

Re: [Freesurfer] mri_convert issues

the error, any more ideas? Best, Jennifer De: freesurfer-boun...@nmr.mgh.harvard.edu en nombre de Tim Schäfer Enviado: jueves, 16 de mayo de 2019 11:50 Para: Freesurfer support list Asunto: Re: [Freesurfer] mri_convert issues External Email - Use Cau

Re: [Freesurfer] mri_convert issues

External Email - Use Caution Dear Jennifer, could it be that you are confusing `mri_convert` and `mris_convert` (note the 's')? Best, Tim > On May 16, 2019 at 10:58 AM jennifer sorinas wrote: > I was trying to convert nifti1 files (.hdr and .img) to nii files using the > com

[Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution Hi! We are getting segmentation fault (core dumped) error when trying to run mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of mri_convert. I suspect that this has to do with libcrypt incompatibilities d

[Freesurfer] mri_convert issues

External Email - Use Caution Hello, I was trying to convert nifti1 files (.hdr and .img) to nii files using the command: > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz But this error pop-up: mri_convert.bin: unknown flag '-i input.hdr' The same command was wo

Re: [Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

Hi Vasudev, are you using an old dev distribution? This was an issue a while back, but it’s fixed now. Andrew From: on behalf of Dev vasu Reply-To: FS Help Date: Thursday, April 25, 2019 at 3:30 PM To: FS Help Subject: [Freesurfer] mri_convert : Error while loading library libGLdispatch.so

[Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0

External Email - Use Caution Dear all, I am trying to convert .mgz file to nii.gz using mri_convert command mri_convert filename.mgz filename.nii.gz but i am getting an error "mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot open shared object file:

[Freesurfer] mri_convert --in_center

External Email - Use Caution Hello, Is it possible to change the origin of the aseg.mgz file? I tried mri_convert --in_center -117 -219 145 aseg.mgz new_aseg.img. When I opened the new_aseg.img file the origin seems to be at 0 -127 0. Any suggestions would be greatly appreciate

Re: [Freesurfer] mri_convert

On 2/21/19 12:56 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, > > Thanks for the response. > yes, I need to extract the acquisition times for kinetic modeling > using PET surfer. Please I have two follow-up questions and I > appreciate any highlights: > -

Re: [Freesurfer] mri_convert

External Email - Use Caution Hi Dr Greve, Thanks for the response. yes, I need to extract the acquisition times for kinetic modeling using PET surfer. Please I have two follow-up questions and I appreciate any highlights: - Are the acquisition times that PET surfer needs to be in

Re: [Freesurfer] mri_convert

you mean you want the acquisition times to do kinetic modeling? I don't have anything to do that. Also, you should check to see whether your PET has intensity scaling imbedded in the dicom as the v6 mri_convert does not handle this properly. On 2/20/19 11:44 AM, john Anderson wrote: > >    

Re: [Freesurfer] mri_convert

External Email - Use Caution mri_convert can do lots of things but I would actually try mri_probedicom to get the DICOM timings. If you have AFNI installed you could also try dicom_hinfo which has more examples in the AFNI wiki than mrI_probedicomi. You could just loop over dicoms

[Freesurfer] mri_convert

External Email - Use Caution hi FS experts. I would like to inquire about the command mri_ convert I use this command to convert fMRI and PET 4D volumes from dicom format to nifti. Are there any flags that can be used in mri_convert command line to enable it to extract a text fi

Re: [Freesurfer] mri_convert

Hi Nazain I can't replicate this problem. Can you verify that the aseg.mgz is correct? If it is, maybe email me those 3 files as well as the complete output of mri_convert? cheers Bruce On Fri, 25 Jan 2019, N Saf wrote: External Email - Use Caution Dear Bruce, I had a prob

[Freesurfer] mri_convert

External Email - Use Caution Dear Bruce, I had a problem with bringing aseg.mgz into my subject space and you recommend this command before: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz which perfectly worked for me but now when I want to try it in new versi

[Freesurfer] mri_convert

External Email - Use Caution Hello, I am working on implementing third party designed code which runs freesurfer via the containerization tool docker. This code runs fine within docker so that it is not the problem. I am attempting to run this same code with a tool named udocker

Re: [Freesurfer] mri_convert trying to find DWI parameters from Philips scans

try export FS_LOAD_DWI=0 (or setenv FS_LOAD_DWI 0 for cshell) On 01/24/2018 02:44 PM, Rockers, Elijah D. wrote: > Hello, > > I am using mri_convert to convert my standard T1-weighted structural > images into nifti format. > > The conversion works, but it might be somewhat delayed due to spammi

[Freesurfer] mri_convert trying to find DWI parameters from Philips scans

Hello, I am using mri_convert to convert my standard T1-weighted structural images into nifti format. The conversion works, but it might be somewhat delayed due to spamming the console with the following message ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: Get

Re: [Freesurfer] mri_convert partial support of nrrd file format for diffusion MRI data

no sorry, we have not tried to support nrrd in years, so I'm not surprised that it does not output bvals/bvecs On 11/29/17 8:10 AM, Michael Dayan wrote: Hi, I was pleasantly surprised when I discovered that mri_convert could convert the nrrd file format (to NIFTI in my case). However for di

[Freesurfer] mri_convert partial support of nrrd file format for diffusion MRI data

Hi, I was pleasantly surprised when I discovered that mri_convert could convert the nrrd file format (to NIFTI in my case). However for diffusion MRI data, while it displays the diffusion gradients information on the terminal, it does not create the associated bval and bvec files. After looking at

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

N Greve > Sent: 13 September 2017 22:44 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault > > Hi Janani, if you want help, please provide more complete information. > Eg, what command was not found? What is the terminal ou

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 13 September 2017 22:44 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault Hi Janani, if you want help, please provide more complete information. Eg, what command was not

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

t; > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: 12 September 2017 21:42 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Seg

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault Do you mean that the error is still there even after running the unsetenv command? And you ran them from the shell, one after the other? On 09/12/2017 02:27 AM, M Janani wrote: > Hi Douglas, > >

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

hanks, > Janani > > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: 12 September 2017 01:25 > To: freesurfer@nmr.mgh.harvard.edu > Subj

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault Try running unsetenv FS_LOAD_DWI then re-running recon-all On 09/11/2017 12:57 PM, M Janani wrote: > > Hi Team, > > Am getting segmentation erro

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Try running unsetenv FS_LOAD_DWI then re-running recon-all On 09/11/2017 12:57 PM, M Janani wrote: > > Hi Team, > > Am getting segmentation error during the > reconstruction process. > > Please help in resolving the error. > > I have attached log

[Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Hi Team, Am getting segmentation error during the reconstruction process. Please help in resolving the error. I have attached log for reference. Thanks, Janani ::DISCLAIMER:: ---

Re: [Freesurfer] mri_convert

MatrixFree: NULL mat POINTER! I am not sure what I am doing wrong. So thank you for help Jon Sent with ProtonMail <https://protonmail.com> Secure Email. Original Message ---- Subject: Re: [Freesurfer] mri_convert Local Time: July 19, 2017 5:12 PM UTC Time: July 19, 2017 9

Re: [Freesurfer] mri_convert

at POINTER! I am not sure what I am doing wrong. So thank you for help Jon Sent with [ProtonMail](https://protonmail.com) Secure Email. > Original Message > Subject: Re: [Freesurfer] mri_convert > Local Time: July 19, 2017 5:12 PM > UTC Time: July 19, 20

Re: [Freesurfer] mri_convert

Hi Jon have you tried mri_convert? cheers Bruce On Wed, 19 Jul 2017, John Anderson wrote: > Dear Freesurfer, > Are there any tools in Freesurfer that can help to convert PET DICOMs to > nifti files? > > Thank you for your help and for any suggestion > Jon > > > ___

[Freesurfer] mri_convert

Dear Freesurfer, Are there any tools in Freesurfer that can help to convert PET DICOMs to nifti files? Thank you for your help and for any suggestion Jon___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/l

Re: [Freesurfer] mri_convert

Hi Doug thank you for the quick response! The source is a Siemens scanner. Data derived from the Spine. I don't know what is the optimal way to convert these ima images to nifti what is the source of the ima file? was it anonymized? You can try something like adding -iid -1 0 0 -ijd 0 1 0 -ikd

Re: [Freesurfer] mri_convert

what is the source of the ima file? was it anonymized? You can try something like adding -iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 but this is just guessing at the orientation On 5/15/17 9:58 PM, John Anderson wrote: Dear Freessurfer experts, i want to convert IMA files to nifti using mri_convert I

[Freesurfer] mri_convert

Dear Freessurfer experts, i want to convert IMA files to nifti using mri_convert I did the following: mri_convert 54365413.ima output.nii I got this error WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing. if I run mri_info on output.nii I see voxel-to-ras dete

Re: [Freesurfer] mri_convert : pix vs no pix ?

When freesurfer reads in an img/hdr file, it makes assumptions about the how the data are oriented, so, implicitly, you are using orientation info. If you do not have a .mat file, then you can't change the header, so you have to change the pixels On 05/09/2017 01:45 PM, Shane Schofield wrote:

Re: [Freesurfer] mri_convert : pix vs no pix ?

Sorry, I don't quite understand yet.. Would the header be important as I am not using img / hdr ? Under what sort of circumstances would pix be favourable? I am using .nii after executing mri_convert to go from img/hdr to nii. I note that pix is used in other older threads too. On Tuesday,

Re: [Freesurfer] mri_convert : pix vs no pix ?

When the pixel data are flipped, you are actually changing the way that the data are stored on disk (while keeping the direction info in the header constant). On 05/09/2017 12:52 PM, Shane Schofield wrote: > Dear Doug, > I am trying to flip some PET images so that they are in the same > orien

[Freesurfer] mri_convert : pix vs no pix ?

Dear Doug,I am trying to flip some PET images so that they are in the same orientation as the T1.I came across this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you explain what what it means to change the pixel data? Should I use pix or without pix? For cont

Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

Many thanks for the answer! Best, Maria 2017-04-25 21:05 GMT+03:00 Douglas Greve : > -i{ijk}s will change the voxel size of the columns, rows, and slices, > respectively > > -i{ijk}d will change the direction cosines of the cols, rows, slices > > > > On 4/25/17 11:47 AM, Maria Hakonen wrote: > >

Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

-i{ijk}s will change the voxel size of the columns, rows, and slices, respectively -i{ijk}d will change the direction cosines of the cols, rows, slices On 4/25/17 11:47 AM, Maria Hakonen wrote: Dear Freesurfer experts, Could someone please let me know what is the meaning of the arguments -

[Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

Dear Freesurfer experts, Could someone please let me know what is the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert? >From the internet and by typing mri_convert on the command line I only managed to find the following information: -iis, --in_i_size -ijs, --in_j_s

Re: [Freesurfer] mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

use mri_vol2vol where you can control the interp. Or, for a binary mask or segmentation, use mri_label2vol On 04/11/2017 03:20 PM, Harris Hoke wrote: > > I’m currently running freesurfer 6.0.0, and I’ve run into the same > problem described in this thread on the archives >

[Freesurfer] mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives . Does anyone know if a fix exists? I'm trying to move binary parcel files from the SPM default MNI152 spac

Re: [Freesurfer] Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

I don't know if this is fixed or not, but you can use mri_vol2vol with the --regheader option and specify the interpolation method with --interp On 03/29/2017 06:25 PM, Harris Hoke wrote: > > I’m currently running freesurfer 6.0.0, and I’ve run into the same > problem described in this thread o

[Freesurfer] Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives . Does anyone know if a fix exists? ~Harris ​ ___ Freesurfer ma

Re: [Freesurfer] mri_convert error: \'GetDICOMInfo(): dcmGetDWIParams() 7\' in FS6.0

When you were getting the error message, was the program continuing? It should have continued normally (though it is not good practice to have big ERROR messages scrolling across the screen:) On 03/01/2017 02:58 PM, Gustav Mårtensson wrote: > > Hi, > > Yes, the buildstamp says > freesurfer-Lin

Re: [Freesurfer] mri_convert error: \'GetDICOMInfo(): dcmGetDWIParams() 7\' in FS6.0

And this is in version 6? What platform are you using? On 03/01/2017 12:07 PM, Gustav Mårtensson wrote: > > Hi, > > Yes, running mri_convert > ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm > > dummy.mgh still produces the error > > ERROR: GetDICOMInfo(): dc

Re: [Freesurfer] mri_convert error: 'GetDICOMInfo(): dcmGetDWIParams() 7' in FS6.0

It looks like it found something that it thinks is a DWI parameter but isn't, and it is causing it to fail. Can you send me one of the dicoms? In the mean time, if you setenv FS_LOAD_DWI 0 then the error should go away On 2/28/17 8:33 AM, Gustav Mårtensson wrote: Hi, I have a problem when

Re: [Freesurfer] mri_convert error message

Hi Robert disk space and permissions are really the only two things I can think of. Can you try writing it somewhere else? Or using .mgz as output (or .nii without the .gz)? cheers Bruce On Wed, 4 Jan 2017, Wujek, Robert wrote: > I'm trying to convert a group of .dcm files to .nii.gz, but I'

[Freesurfer] mri_convert error message

I'm trying to convert a group of .dcm files to .nii.gz, but I've been getting the following output with an error at the end... mri_convert IM-0020-0001.dcm example.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM-0020-0001.dcm... Starting DICOMRead2() dcmf

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

r-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, December 6, 2016 2:04 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz > > Not sure. This one did not look like a mosaic (it had 256x256 voxels). &

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

RIcron. Thanks, Marianna -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, December 6, 2016 2:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert dcm 'Mos

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

RIcron. Thanks, Marianna -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, December 6, 2016 2:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert dcm 'Mos

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, December 6, 2016 12:59 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz > > This file is missing critical information. Did this come directly from your > scan

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

ginal Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, December 6, 2016 12:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz This file is m

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve > Sent: Tuesday, December 6, 2016 10:23 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

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