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some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
by zlseu2109 10 Jul '23

10 Jul '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu FROM: zlseu2109(a)163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers, I’ve segmented thalamic nuclei via thalamic nuclei atlas (https://secure-web.cisco.com/1WjR2s5Zpo0C0UoA2TqjDmB6EwtzK0RI_lg2slhweQFKPQ…) and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal) | | zlseu2109 | | zlseu2109(a)163.com |

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ill-conditioned matrix problem
by 조상아 09 Jul '23

09 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I have a question. I'm attempting to run an estimation with my subjects (tic patients versus controls) and get stuck with an ERROR: matrix is ill-conditioned or badly scaled, condno = 31219.4 As covariates, we included three variables ( age, IQ, Total intracranial volume ). We added our matrix file as an attached file - lh-Avg-thickness-age-Cor.mtx. The number of regressors are 16 (The number of classes 4) * ((The number of continuous covariates=3) + 1)=16. I've searched the list for the similar cases and found no answers reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the fsgd , matrix file, and error screen-captured. 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 2) Platform: ubuntu 22.04 3) uname -a: Linux capneurodata-5950x 5.19.0-46-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

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problem with infantfreesurfer
by Knut J Bjuland 09 Jul '23

09 Jul '23

External Email - Use Caution Dear Freesurfer expert I have found this problem when I am running infant freesurfer on newborn mri image. Best regards Knut Jørgen Bjuland mri_convert --conform /home/knutjb/subjects/EPOP510_fs/work/mprage.nu.conf.nii.gz /home/knutjb/subjects/EPOP510_fs/work/sscnn/conformed.nii.gz WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (316.00 mm, 316.00 mm, 316.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 316 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++=============== reading from /home/knutjb/subjects/EPOP510_fs/work/mprage.nu.conf.nii.gz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998888, 0.0471505, 5.29093e-11) j_ras = (-0.0107408, -0.227545, -0.973708) k_ras = (0.0459108, 0.972625, -0.227799) Reslicing using trilinear interpolation writing to /home/knutjb/subjects/EPOP510_fs/work/sscnn/conformed.nii.gz... [<tf.Tensor 'bnorm_D_1_00_1/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_1/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_1/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_1/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_1/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_1/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_1/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_1/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_1/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_1/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_1/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_1/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>] 12 Loaded model file: /usr/local/infantsfreesurfer/average/sscnn_skullstripping/cor_sscnn.h5 2.073170731707317 Image max is :2.0650406504065044 Traceback (most recent call last): File "/usr/local/infantsfreesurfer/python/scripts/sscnn_skullstrip", line 74, in <module> cor_img_data = predict('cor') File "/usr/local/infantsfreesurfer/python/scripts/sscnn_skullstrip", line 70, in predict net.predict_slice_segmentation([conformed_file], [args.contrast], direction_fullnames[direction], out_membership_file, out_hard_file) File "/usr/local/infantsfreesurfer/python/packages/sscnn_skullstripping/deeplearn_utils/DeepImageSynth.py", line 807, in predict_slice_segmentation out_slices = self.model.predict(input_feature_array) File "/usr/local/infantsfreesurfer/python/lib/python3.6/site-packages/keras/engine/training.py", line 1147, in predict x, _, _ = self._standardize_user_data(x) File "/usr/local/infantsfreesurfer/python/lib/python3.6/site-packages/keras/engine/training.py", line 749, in _standardize_user_data exception_prefix='input') File "/usr/local/infantsfreesurfer/python/lib/python3.6/site-packages/keras/engine/training_utils.py", line 137, in standardize_input_data str(data_shape)) ValueError: Error when checking input: expected input_ax to have shape (256, 256, 1) but got array with shape (316, 316, 1)

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Re: [Freesurfer] Problem accessing Buckner40 dataset
by fsbuild 06 Jul '23

06 Jul '23

External Email - Use Caution It looks like Mr. Buckner has moved on from where the link points to on that web site, i.e., that link is no longer valid.  His current lab posts this link for tools and data,cnl.rc.fas.harvard.edu/data-tools - but it’s not clear to me the same subjects are available there.   I don’t believe we can  re-distribute our pre-existing in-house copy.- R. On Jul 6, 2023, at 12:39, vinuyan sivakolunthu <vinuyansivakolunthu(a)gmail.com> wrote:        External Email - Use Caution        Hello Freesurfers,I was trying to access the Buckner40 dataset. There is a fswiki page (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1z4yAeqKJPyvFsObHdvqaJln_dwai7U-KJwGI2DQuNZcPN…) that points to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1HJMRA3U3EHGopGkvJohIBU6zqAVrXsd6MgZX2fBDDJmOia…, but the site is no longer up. Is there somewhere else where I could obtain the data?Thanks,Vin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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free surfer gets stuck infinitely during recon-all
by Rona Haker 06 Jul '23

06 Jul '23

External Email - Use Caution I'm attempting to do a full brain segmentation for a subject in my study using recon-all but after hours of running it did not reach the final step of creating aparc+aseg (the file I need), even though no error was printed. The last file that was created was 14 hours ago (till I stopped the run manually just now). my command is: recon-all -s ./00_FSseg -i ./8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all Attached is the log report of the run. By the way, this is a subject I have tried 3 times already to segment with no success, although most subjects in my study succeeded on the first try. recon-all -version command outputs this: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thank you, Rona Haker

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Regarding the paper on SYNTHSR... accuracy of parcellations?
by KennethSPrice 05 Jul '23

05 Jul '23

External Email - Use Caution Hello Freesurfers, I recently read the paper titled "SYNTHSR: A PUBLIC AI TOOL TO TURN HETEROGENEOUS CLINICAL BRAIN SCANS INTO HIGH-RESOLUTION T1-WEIGHTED IMAGES FOR 3D MORPHOMETRY" and need more information regarding table 2 (attached). Pearson Correlation values were given for SEGMENTATION structures but not PARCELLATION structures. Surely these values must be available somewhere? Could you please post the PARCELLATION correlation values? Thanks, Ken.

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requesting password for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Ranjini Garani Ramesh 05 Jul '23

05 Jul '23

External Email - Use Caution Hi, I am requesting the password to extract "FS_7_2_0_ubuntu_18_04_06.ova.7z". Regards Ranjini

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Longitudinal Pipeline Issue
by Atwater, Emanuel R 05 Jul '23

05 Jul '23

External Email - Use Caution Hello Freesurfer Team I'm attempting to create the base for the longitudinal scan process, as described in the Longitudinal Tutorial (https://secure-web.cisco.com/1nkZqRPPwsOtKx4RoeA_xG1zIjqnnyVHLQdZ7CBucl4swE…) but for some reason I am unable successfully complete the base. FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Recon-all.log: see attached V/r, Emanuel Atwater

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Variation in volume when recon-all is run 1416 times on the same subject
by 神保岳大 05 Jul '23

05 Jul '23

External Email - Use Caution Dear FreeSurfer team, We were interested in the reproducibility of multiple runs of recon-all and repeated recon-all 1416 times on the same subject. We then checked the left and right brain results for the volume obtained from the Aseg process. The right brain showed exactly the same volume, while the left brain showed a small variation. We thought that the variation in volume between the left and right brains would be the same. But why is this not the case in reality? The volume_attemps1416.csv is attached. For example, the Left-Lateral-Ventricle in this file has variation, but the Right-Lateral-Ventricle has no variation, as shown below. *Left-Lateral-Ventricle*12377.8 12375.9 12375.9 12380 12376.4 ... *Right-Lateral-Ventricle*7514.7 7514.7 7514.7 7514.7 7514.7 ... 1) FreeSufer vesion: 7.2.0 2) Platform: Red Hat Enterprise Linux 8.6 3) uname -a: Linux fn01sv01 4.18.0-372.36.1.el8_6.x86_64 #1 SMP Thu Nov 17 16:37:07 EST 2022 x86_64 x86_64 x86_64 GNU/Linux 4) volume_attemps1416.csv: Summarized results of 1416 aseg.stats.

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dcmunpack: Issues with the -run argument
by Sara Teso Cuesta 03 Jul '23

03 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use dcmunpack to transform dicom images to a nifti format inside a FSFAST formatted directory ( https://secure-web.cisco.com/1JV-FemocV4fiLoKofgFHZ2hQTt_nlpR8LAqJEXvFr3d88…) however I am having issues understanding how to use properly the -run argument. This is the command I am trying to use: dcmunpack -src fMRI_dir -targ sessionid -fsfast -run 2 rest nii.gz f.nii.gz I assume I am making some mistakes with the command, specially with the run arguments since this is the error that I got in the terminal: ERROR: could not find run 2 in data My directory contains fMRIs downloaded directly from the ADNI database and grouped in folders following this structure: /fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to solve this? 1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb 2) Platform: Ubuntu 20.04 in WSL Thanks for your help.

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