External Email - Use Caution Dear Yujing,
Thank you kindly for your support. Please see attached. Kind regards, Rebecca Downloads.zip <https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing *Sent:* Tuesday, 26 April 2022 8:34 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] recon-all error Hi Rebecca, We would like to understand why those dicom files are not recognized by Freesurfer. If it is possible, can you provide us some of those dicom files to debug? Thanks. Yujing *From:* freesurfer-boun...@nmr.mgh.harvard.edu < freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing *Sent:* Saturday, April 23, 2022 1:50 PM *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] recon-all error Hi Rebecca, Thank you for the information. I'm wondering if you would like to try converting those dicom using dcm2niix to .nii, and then feed .nii to recon-all pipeline. You can download dcm2niix here: https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix I use the following command to do conversion: dcm2niix -o <output dir> -f "%s_%p" <dicom dir> Please note that <dicom dir> needs to be specified as last parameter. '-f <>' specifies output file name format - "%s_%p" will have series no + protocol as prefix. Hope these helps. Best, Yujing ------------------------------ *From:* freesurfer-boun...@nmr.mgh.harvard.edu < freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of coope...@student.unimelb.edu.au <coope...@student.unimelb.edu.au> *Sent:* Saturday, April 23, 2022 2:44 AM *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] recon-all error * External Email - Use Caution * Hi Yujing, I guess not. This is the output: cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ mri_probedicom --i /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 is not a dicom file or some other problem Entering IsDICOM (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256) ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 is not a dicom file or some other problem I also ran straight to the dicom files themselves, with the same response: cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ mri_probedicom --i /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 is not a dicom file or some other problem Entering IsDICOM (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001) Opening /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 as part10 DCM_FILEOPENFAILED 20092 DCM failed to open file: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 in DCM_OpenFile Opening as littleendian DCM_FILEOPENFAILED Opening as bigendian DCM_FILEOPENFAILED Opening as format conversion DCM_ILLEGALOPTION Leaving IsDICOM (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001) ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 is not a dicom file or some other problem Thank you, Rebecca *From:* freesurfer-boun...@nmr.mgh.harvard.edu < freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing *Sent:* Friday, 22 April 2022 11:11 PM *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] recon-all error Hi Rebecca, I’m wondering if the dicom files are being recognized. Can you run the following command with some dicom files in the directory? mri_probedicom --i <your_dicom_file> --d filetype (Replace <your_dicom_file> with full path to dicom file.) Thanks. Yujing *From:* coope...@student.unimelb.edu.au <coope...@student.unimelb.edu.au> *Sent:* Friday, April 22, 2022 1:34 AM *To:* Huang, Yujing <yhuan...@mgh.harvard.edu>; 'Freesurfer support list' < freesurfer@nmr.mgh.harvard.edu> *Subject:* RE: [Freesurfer] recon-all error * External Email - Use Caution * Dear Yujing, Thank you for your reply. 1. Confirmed I am running Freesurfer 6.0. 2. I am running both commands from within the individual subject directory (ID=1003156). The parent folder contains several folders all labelled with different subject IDs, and within each contains the dicom directories. 3. I attempted this and received the error: /Applications/freesurfer_v6/bin/dcmunpack -src /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/ -rwxr-xr-x 1 chesterk admin 23759 Jun 14 2018 /Applications/freesurfer_v6/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Fri Apr 22 15:32:30 AEST 2022 Fri Apr 22 15:32:30 AEST 2022 Found 114 total files. Interrogating each and every one of them. Be patient. If you have collected the data in the Martinos center, this will run faster if you kill this job and re-run with -martinos Except, with changes in the file naming (Oct 2012), this does not work. cat: /tmp/dcmdir-all.23294: No such file or directory Found 0 unique series: Patient: Undefined variable. With thanks, Rebecca *From:* Huang, Yujing <yhuan...@mgh.harvard.edu> *Sent:* Friday, 22 April 2022 4:19 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Cc:* coope...@student.unimelb.edu.au *Subject:* RE: [Freesurfer] recon-all error Hi Rebecca, I’m trying to get more information to determine how it core dumped. 1. Can you confirm that you are running Freesurfer 6.0? 2. >From which directory, did you run recon-all and dcmunpack? 3. Can you try dcmunpack by passing it full path to dicom directory? Thanks. Yujing -------- Forwarded Message -------- *Subject: * [Freesurfer] recon-all error *Date: * Sun, 10 Apr 2022 07:01:30 +1000 *From: * coope...@student.unimelb.edu.au *Reply-To: * Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> *To: * freesurfer@nmr.mgh.harvard.edu * External Email - Use Caution * Dear FreeSurfer developers, I’m attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I’ve also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper The information in this e-mail is intended only for the person to whom it is addressed. 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