Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

4 11

mri_watershed and improvements of skullstripping
by Michelangelo Fabbrizzi 01 Feb '24

01 Feb '24

External Email - Use Caution Dear Freesurfer experts, I am new to FS, and I would have couple of questions. I used in sequence: A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1 B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate wrong BEM surfaces; even using -h 5 the result is not optimal: mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz I am wondering: - how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one? - is it possible to use the -gcut command also for mri_watershed? Thanks, appreciated, Miche

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Tkregister2 GUI not responding fully
by Viktorija Pratuseviciute 02 Nov '23

02 Nov '23

External Email - Use Caution Hello, We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (https://secure-web.cisco.com/1acx6rTd53-Vz7knc_wTrpqifC8PTuiKKanQydzd8QVOyX…) The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output? We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results. Many thanks, Viki

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Re: [Freesurfer] MANCOVA + Posthoc Testing Design Matrix Setup
by Cristina A. F. Román 15 Oct '23

15 Oct '23

External Email - Use Caution Hello, I am looking to run a MANCOVA to examine cortical gray matter differences across three groups (accounting for several covariates), and I was hoping to get input on whether I am setting up my design matrix correctly. Groups: 3 Covariates: Age (demeaned), disease duration (DD; demeaned), sex Simplified Example: Group EV1(Grp1) EV2(Grp2) EV3(Grp3) EV4(age) EV5(DD) EV6(sex) 1 1 0 0 0.25 0.75 -1 1 1 0 0 0.25 0.25 -1 1 0 1 0 -0.75 -0.25 1 1 0 1 0 0.5 -0.75 1 1 0 0 1 -0.5 0.5 1 1 0 0 1 0.25 0.25 -1 Questions: 1. Is this an appropriate way to do a three-group comparison with covariates? Or, is it better to just run three separate t-tests (including covariates)? 2. Regarding post-hoc testing, would I just do three separate t-tests? This issue here, I imagine, is that the individual t-test results may not reflect the original MANCOVA results (e.g., post-hoc testing reveals a new significant area that was not significant in the MANCOVA). 3. One other option is to run the initial MANCOVA within a statistical program (i.e., using global cortical gray matter volumes) and then follow up with postdoc testing within FSL (i.e., t-tests). Would this make sense? Thanks in advance for your time and help, Cristina

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Question about mri_nu_correct.mni
by ruifeng14＠gmail.com 15 Oct '23

15 Oct '23

External Email - Use Caution Hi all, I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with 176*256*256 FOV, 1mm isotropic resolution. I saw that the Ants N4 bias correction is done after the FOV is expanded to 256*256*256, not on the original image. Shouldn't the zeros in the expanded image affect the bias correction? Thanks. Best, Ruifeng

2 1

SAMSEG choice of the input
by Giulio Siracusano 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Experts, I'm trying to understand what is the best input choice for running SAMSEG --recon in order to have the closest results as possible when compared against ASEG after executing (separately) an instance of recon-all all (and the raw input files in NIFTI format). I'm very well aware that ASEG and SAMSEG are different methods. I'm using the aseg.stats file as a results of the recon-all all command (here renamed as aseg.recon-all.stats for an easier identification). These stats should be my reference. Currently I've run the samseg command using the following input variants: 1) raw input file (brain MP-RAGE sequence) converted into a mgz archive (Raw.mgz). samseg --t1w ./Raw.mgz --s 002_S_0685_DIRECT --recon --refmode t1w The corresponding results are attached into (samseg.direct.stats) 2) This time I've used the file T1.mgz which is one of the intermediate results generated after running recon-all -autorecon 1. Specifically, this is the output of (mri_normalize <https://secure-web.cisco.com/1JV3nYNrViePm1qpOtzuMUtCndnVtCut-gp7OyXxNuXIOk…> -g 1 -mprage nu.mgz T1.mgz). samseg --t1w ./T1W/T1.mgz --s 002_S_0685_DIRECT_T1W --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.direct.t1.stats). 3) this time I've used the file brainmask.mgz which is the last intermediate result generated after running recon-all -autorecon 1. Specifically, this is the output of mri_watershed <https://secure-web.cisco.com/1DjG5BDGTEbHYOWKmd4lc63SOmX8IrmziV9_NRWhpCskwO…>. samseg --t1w ./brainmask.mgz --s 002_S_0685_DIRECT_BRAIN --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.brain.stats). I've noticed that the SAMSEG stats file (samseg.brain.stats) as obtained when using the brainmask.mgz as input file is the closest with the ASEG statistics (aseg.recon-all.stats). I also observe that the unknown volume is the lowest (# Measure Unknown, 5329.102436, mm^3) when using brainmask.mgz as input for SAMSEG, whereas is higher (Measure Unknown, 325302.894793, mm^3) when using T1.mgz as input file and is the highest (Measure Unknown, 946924.354060, mm^3) for the raw input. I know that for running recon-all we use the raw input files (for example, in NIFTI format), but I wanted to know what is the best possible configuration for SAMSEG in terms of input file in order to have the closest match between SAMSEG and ASEG statistics. Could it be possible to use the intermediate result T1.mgz or brainmask.mgz as input file for running samseg command? Is it a technically correct procedure? Do we need to use only the raw data as input for running samseg --recon command? Hope this is clear Regards GS

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recon-all-clinical out of memory error
by Matthew Lynch 10 Aug '23

10 Aug '23

External Email - Use Caution I am having trouble running the new recon-all-clinical module. I input 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be an out of memory error. I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a computer with 16 Gb RAM. Can anyone provide any thoughts on how to correct this? Thanks in advance! Here is the command: recon-all-clinical.sh ./T1AX5MM/119 fsclin 1 here is the error output: SynthSeg-robust 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 the following problem occured with image /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz : Traceback (most recent call last): File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in predict post_patch_segmentation, post_patch_parcellation, qc_score = net.predict([image, shape_input]) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 70, in error_handler raise e.with_traceback(filtered_tb) from None File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/tensorflow/python/eager/execute.py", line 52, in quick_execute tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name, tensorflow.python.framework.errors_impl.ResourceExhaustedError: Graph execution error: Detected at node 'model_5/unet_parc_merge_8/concat' defined at (most recent call last): File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 2642, in <module> main() File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 162, in main predict( File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in predict post_patch_segmentation, post_patch_parcellation, qc_score = net.predict([image, shape_input]) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2382, in predict tmp_batch_outputs = self.predict_function(iterator) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2169, in predict_function return step_function(self, iterator) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2155, in step_function outputs = model.distribute_strategy.run(run_step, args=(data,)) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2143, in run_step outputs = model.predict_step(data) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2111, in predict_step return self(x, training=False) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 558, in __call__ return super().__call__(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py", line 512, in call return self._run_internal_graph(inputs, training=training, mask=mask) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py", line 669, in _run_internal_graph outputs = node.layer(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/layers/merging/base_merge.py", line 196, in call return self._merge_function(inputs) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/layers/merging/concatenate.py", line 134, in _merge_function return backend.concatenate(inputs, axis=self.axis) File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/backend.py", line 3581, in concatenate return tf.concat([to_dense(x) for x in tensors], axis) Node: 'model_5/unet_parc_merge_8/concat' OOM when allocating tensor with shape[1,256,256,160,72] and type float on /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu [[{{node model_5/unet_parc_merge_8/concat}}]] Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info. This isn't available when running in Eager mode. [Op:__inference_predict_function_10473] resuming program execution

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Freesurfer version and Installation
by hmarzban＠student.ubc.ca 08 Aug '23

08 Aug '23

External Email - Use Caution Dear Freesurfer developers, Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to locate the source file on your website. Could you kindly guide me to where I can find the mentioned version? Alternatively, if this specific version is no longer available, please advise me on which version I should download and install to achieve the same results as before. Thank you very much for your assistance. Regards Hengameh

1 1

cortical boundary and center of gravity
by Alexandra.Korda＠uksh.de 07 Aug '23

07 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I need to compute the distance between the center of the mass in grey matter images and the cortical boundary. Then, I need this spatial-series to be saved in a csv. It is also possible to save the cortical boundary series and the center of gravity and then externally calculate the distances. I've searched for it in the archived question but I didn't find anything similar. Looking forward to your response. With kind regards, Dr. -Ing. Alexandra Korda Forschung & Lehre Zentrum für Integrative Psychiatrie ZIP gGmbH Campus Lübeck Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck Tel.: +49 451 500-98715 alexandra.korda(a)uksh.de<mailto:mihai.avram@uksh.de> I http://secure-web.cisco.com/1kjPgsmVDmckwQECyP-u3VHis_G3UTBRfaGW5nBWnoOZ_A6…<https://secure-web.cisco.com/1YbIIElV63eryvTPycz1rwlHnTXCKH5QIVHqvKeuBQOTbv…> https://secure-web.cisco.com/1LBiUwtsltNc-BXRSlxA10cSmuxQKqQl4sLcRE1H3NCCq2… [https://secure-web.cisco.com/1AOOsqucbGmTeJdM-yAtUPIzv7tfFlnW2B7m613-b26KYy…]<https://secure-web.cisco.com/1sCPy2VI9VIeqBFD-78XnzcpPLre5X30Ap7YIpu2wGcBlc…> UKSH hilft Ukraine: Wir machen weiter. Helfen Sie uns, zu helfen! Unterstützung für die Menschen in und aus der Ukraine. UKSH-Gutes tun!-Spendenkonto zur Aktion Empfänger: UKSH WsG e.V. IBAN: DE75 2105 0170 1400 1352 22 | BIC: NOLADE21KIE Angabe bei Ihrer Überweisung im Verwendungszweck: FW14042: UKSH hilft Ukraine Spenden via PayPal: Spenden per PayPal<https://secure-web.cisco.com/19zuU7kAXVZctDul3KKV_Or91foAK2DNNZElMPDJPSvwoO…> Alle Infos: http://secure-web.cisco.com/1Yp2GziezQ--zorAWLWgh3JZPDvYVbGWcPyrW9Oj_shCvKt…<http://secure-web.cisco.com/1Yp2GziezQ--zorAWLWgh3JZPDvYVbGWcPyrW9Oj_shCvKt…> [UKSH logo] Universitätsklinikum Schleswig-Holstein Rechtsfähige Anstalt des öffentlichen Rechts der Christian-Albrechts-Universität zu Kiel und der Universität zu Lübeck Vorstandsmitglieder: Prof. Dr. Dr. h.c. mult. Jens Scholz (Vorsitzender/CEO), Peter Pansegrau (CFO), Corinna Jendges (COO), Prof. Dr. Thomas Münte, Prof. Dr. Joachim Thiery Vorsitzender des Aufsichtsrates: Guido Wendt Bankverbindungen: Förde Sparkasse IBAN: DE14 2105 0170 0000 1002 06 SWIFT/BIC: NOLA DE 21 KIE Commerzbank AG IBAN: DE17 2308 0040 0300 0412 00 SWIFT/BIC: DRES DE FF 230 Gemeinsam Gutes tun! Spenden: Alle UKSH-Spendenmöglichkeiten unter http://secure-web.cisco.com/1PM4Bl_XCW2TI9S7xBSfxsI0bNs2hyeV1XHLSi6-EhvbIpx…<http://secure-web.cisco.com/1PM4Bl_XCW2TI9S7xBSfxsI0bNs2hyeV1XHLSi6-EhvbIpx…> Spendenkonto: Förde Sparkasse IBAN: DE75 2105 0170 1400 1352 22 | BIC: NOLADE21KIE | Empfänger: UKSH WsG e.V. Diese E-Mail enthält vertrauliche Informationen und ist nur für die Personen bestimmt, an welche sie gerichtet ist. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, bitten wir Sie, uns hiervon unverzüglich zu unterrichten und die E-Mail zu vernichten. Wir weisen darauf hin, dass der Gebrauch und die Weiterleitung einer nicht bestimmungsgemäß empfangenen E-Mail und ihres Inhalts gesetzlich verboten sind und ggf. Schadensersatzansprüche auslösen können.

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How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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