Freesurfer

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30067 discussions

Affine Transform to Talairach Failed
by QL X 20 Aug '23

20 Aug '23

External Email - Use Caution Dear list: I want to use freesurfer to do the preprocess, transform the image to Talairach space. I use the recon-all command with autorecon1 and obtain the talairach.xfm file. Then I use mri_convert with --apply_transform option. Here's the code I used: ``` recon-all -parallel -i $sample_path -autorecon1 -subjid $sample_name -cw256 mri_convert --apply_transform mri/transforms/talairach.xfm \ mri/brainmask.mgz \ mri/brainmask_align.mgz ``` This operation moves the brain outside of the image boundary: [image: image.png] I also tried this which is suggested by freesurfer mri_convert documentation: ``` mri_convert --apply_transform mri/transforms/talairach.xfm \ -oc 0 0 0 \ mri/brainmask.mgz \ mri/brainmask_align.mgz ``` But the brain shape is weird and still some part of it is out of boundary: [image: image.png] I'm not sure why this happens. I didn't notice any errors when using autorecon1 command. I have checked recon_all.log and the program finished without error. What should I do to transform the image to Talairach space correctly? Looking forward to your reply. Best regards, gyddhpy [image: Mailtrack] <https://secure-web.cisco.com/1FgOh-kgul0oJnTKW_HJ-Y6578cTV4_OlVhajI96G-Utzr…> Sender notified by Mailtrack <https://secure-web.cisco.com/1FgOh-kgul0oJnTKW_HJ-Y6578cTV4_OlVhajI96G-Utzr…> 23/08/13 12:20:38

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Re: [Freesurfer] recon-all-clinical out of memory error
by fsbuild 19 Aug '23

19 Aug '23

External Email - Use Caution You might be better off with swapping inside the Linux VM instead of on the windows host.  Or I don’t see anything preventing the Windows host from trying to swap out the entire VM process - which I would not expect to be efficient.  You only need the application running *inside*the*Linux*VM* to be swapped out if necessary (using the Linux OS to do that). This should be straightforward to setup using VirtualBox to run the Ubuntu Linux VM we provide with Freesurfer already installed, i.e., download fromhttps://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 In the screenshot below, the FreeSurfer VM starts with 4G allocated to it.  So correspondingly, inside the VM the “free” command reports there is ~4G available of which only 1G is being used since nothing consequential is running.  If you stopped the VM, increased the allocated memory in the VirtualBox application, and re-started the VM, you would see the total available memory scale up accordingly. For available swap space, you would look at the boot image on /dev/sda1.  That image is made on purpose as small as possible so it can grow and/or space can otherwise be used.  The “df” commands shows that out of the box, the VM takes up 22G of the max allowed size of 170G.  That leaves potentially 170-22=148G to be used for other purposes.  You certainly would not want to allocate all that for swap space, but there is space to use for a good chunk of swap space apart from space you will consume doing work that adds files into the VM.   Here is 1 of many articles about setting up swapping in VirtualBox (which we do not setup by default),https://secure-web.cisco.com/1SoOpwrbWi8O6Ms8nTQEeN2LjbgQTjyi2PtBS… The efficiency of swapping will be limited by your system, e.g., how fast the disks are, their bus interface, etc.  There’s no guarantee even the most efficient swap configuration won’t cause the machine to slow down to a crawl depending upon what you are processing.  It’s not a substitute for having RAM to allocate to the VM.   We have discussed increasing the published memory system requirements for Freesurfer. - R. On Aug 13, 2023, at 06:39, Matthew Lynch <matthewl077(a)gmail.com> wrote:        External Email - Use Caution        The method I mentioned before does not always work.  It worked for all but about 3 scans out of approximately 30.  There are some scans for which the "committed memory" caps at about 23 Gb in the task manager and then either the out of memory error occurs or the WSL session is killed.  Increasing the .wslconfig swap and memory beyond 32 Gb didn't work.  Increasing the Windows pagefile size to 8 Gb didn't work.  The output of free -h during the synthseg run was 0Gb used, 40Gb free, which seems to suggest it is not using the swap.  I suspect this is a matter of somehow getting WSL to properly use large amounts of swap space.On Thu, Aug 10, 2023 at 5:52 PM fsbuild <fsbuild(a)contbay.com> wrote: Hello Matthew,Thanks for this info.If it is not too much work, just wondering if you could make a rough estimate or compute an average for the *total*memory* in use = (size of physical RAM in use by synthseg + size of all swap files resident on disk used by synthseg).- R.On Aug 10, 2023, at 16:08, Matthew Lynch <matthewl077(a)gmail.com> wrote:        External Email - Use Caution        Here is some additional follow up.  I was able to get recon-all-clinical working in Ubuntu in WSL on a 16 Gb machine by increasing the swap and memory allowed in WSL..  This is done through the .wslconfig file which is located in the %USERPROFILE% folder (e.g. C:\Users\username\).  I had to specify a swap size of 32 Gb and also specify that WSL is allowed to use 32 Gb (even though the system only has 16 Gb -- it will use swap space).Here is the .wslconfig file I used:-----[wsl2]# Limits VM memory to use no more than x GB, this can be set as whole numbers using GB or MB# This must be set to 32 Gb or so to accomodate recon-all-clinical# If you set a 32 Gb swap but not 32 Gb memory allowance, WSL will stop at the memory limit and not use swapmemory=32GB # Sets amount of swap storage space to 8GB, default is 25% of available RAMswap=32GB# Sets swapfile path location, default is %USERPROFILE%\AppData\Local\Temp\swap.vhdx# I believe the double backslash is necessaryswapfile=P:\\Users\\username\\WSL\\wsl-swap.vhdx------For information on the .wslconfig file, see: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1YhCioZJWCu0zXeYK4niBT1mPiOvP3-iZtJpGr… Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch <matthewl077(a)gmail.com> wrote:I was able to get recon-all-clinical working with 16 Gb computer.I thought the problem might be Windows hogging memory, so I created a live persistent USB install of lubuntu, using lubuntu 22 as a low resource distro in order to minimize memory usage, and installed freesurfer 7.4.0.  Even with initial memory usage on 1Gb on lubuntu, synthseg still failed with out of memory error with 8 Gb swap file.  I watched the swap memory fill up and then process was killed.I added 16Gb swap using the following instructions, for a total swap space of 24 Gb + 16 Gb memory:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WPE5E2926p5mVe9dnrOA4IZD9X-ZV99yY22Yp… worked.On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch <matthewl077(a)gmail.com> wrote:I do not have access to a computer with more RAM.  I can run recon-all with 1mm T1 images without any problems.  How much RAM would recon-all-clinical be expected to need?  Does it require less RAM if it uses the GPU instead of CPU?  On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Can you try it on a computer with more ram?  From: freesurfer-bounces@nmr..mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Matthew LynchSent: Thursday, July 13, 2023 1:55 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all-clinical out of memory error         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 2.0using CPU, hiding all CUDA_VISIBLE_DEVICESusing 1 threadpredicting 1/1the 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 _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RM958Qv9v8qGhZdH49O5-gI0p7sKgqtIF4Hpl… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tNH98Dri_B6JdnDtuaRGNNkqOO4pdnTL51DT_… has detected a possible fraud attempt from "secure-web..cisco.com" claiming to be https://secure-web.cisco.com/1ZANIKFhlE3Lxednpj2HqYjNbeSPtXtn9tPydk…; ._______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Installation tensorflow: protobuf requires Python '>=3.7' but the running Python is 3.6.8
by fsbuild 18 Aug '23

18 Aug '23

External Email - Use Caution Hello Joost, It looks like you are using an old 2020 development build prior to fspython being updated to version 3.8.X with a newer version of tensorflow installed. The latest 7.4.1 release from June 2023 should have a tensorflow version 2.12 installed.  You can download that and other releases from,https://secure-web.cisco.com/1W23QRgkV4lyrjm7TGpfUuJAucD3HfZxXV6cIIM0a… We recommend using a release build since those are more thoroughly tested and expected to be more stable compared to the development builds (e.g., what you listed).  But if you need to use something that can only be found in the latest development builds, those can be downloaded via the link below.  The tensorflow version has been updated to 2.13 in development builds.https://secure-web.cisco.com/1WgPel729y72zSVXgE1wFN5HV9jv9DpJYQXKCX3… The freesurfer builds/releases are tested with the accompanying fspython distribution and setup to not encourage modifying that tested setup.   Since “fspython” is independent of finding “python” in your PATH, then after you source the freesurfer environment setup script, I believe it is possible to change what python gets run.  If you really need to do that,  we can follow up with you. - R.

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Zero-Interpolation Filling DWI TRACE
by Sorby-Adams, Annabel 17 Aug '23

17 Aug '23

External Email - Use Caution Dear Freesurfer aficionados, I am generating b900 TRACE images from 3 diffusion directions acquired at low-field. I was wondering if there are any zero-filling/padding options so I can try to interpolate my images to improve resolution (which is already compromised at low-field), such as via mri_convert? Thanks! Annabel

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Longitudinal Processing Stream Version
by Sunavsky's Stocks 17 Aug '23

17 Aug '23

External Email - Use Caution Hello, I have a question about longitudinal stream processing. On the wiki page ( https://secure-web.cisco.com/1ak_FVO1o5iVON2RkYI_Y4g9zeL4DobzwWVTa4pFlVvLOZ…) it states that you can do longitudinal processing up to version 6.0 of FS. I was wondering if later versions of FS (7.4.x) can also be used to do longitudinal processing. Thank you for your help, Adam.

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mailing list
by Pavlina.Pokosova＠fnmotol.cz 17 Aug '23

17 Aug '23

1 0

Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS
by fsbuild 16 Aug '23

16 Aug '23

External Email - Use Caution  Since that did not work, I suggest you try some of the other suggestions in that posting about changing the permissions on files related to _apt..  If you are not a system administrator, then perhaps one could help you out.  It reads to me like different fixes worked for various people depending upon their system.  You could check to see if there are any Ubuntu system updates available as that might help, but I don’t see any reports of that providing a fix.  I would expect what you list to happen with any binary RPM you download and try to install, i.e., I don’t see this as an issue with the freesurfer installer. - R. On Aug 16, 2023, at 06:19, Praise Matsekete <MTSPRA001(a)myuct.ac.za> wrote:        External Email - Use Caution        Good day,Kindly find attached a screenshot of what I tried to do in the terminal as well.Kind regards,Praise From: Praise Matsekete <MTSPRA001@myuct.ac.za>Sent: Wednesday, 16 August 2023 12:08To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS Good day,Thank you so much for the help. I tried to "chmod 777" the .deb file before  installing it. However, I am still experiencing the same issue.Kindly find attached a copy of the text from the terminal after I tried this.Kind regards,Praise MatseketeFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild@contbay.com>Sent: Tuesday, 15 August 2023 21:48To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Praise Matsekete <MTSPRA001@myuct.ac.za>Subject: Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS CAUTION: This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source.        External Email - Use Caution        Hello Praise,This post,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://askubuntu.com/questions/908800/what-does-this-apt-error-message-d… indicates it is from a permission problem with _apt on the system (which may have been an Ubuntu bug/issue).    One of the more innocuous fixes suggested there is to down protect or “chmod 777” the .deb package and then try to install it.  Other fixes involve changing the permissions of system files.  I have not seen that error testing the install in a newly made Ubuntu 22 docker container.- R.On Aug 15, 2023, at 10:43, Praise Matsekete <MTSPRA001(a)myuct.ac.za> wrote: Download is performed unsandboxed as rootDisclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://secure-web.cisco.com/1n1CU5pgJva0i88ZdZvGUVVJvFn05Or9gojbkdZVXUZHyo4… or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://secure-web.cisco.com/1ZM9iFYqL-twUClMROcbvwPaSPzsAlYMRElsr6iQpdf2UI… from 2023-08-16 12-04-10.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Password for unzipping virtual machine image
by Jochen Ditterich 16 Aug '23

16 Aug '23

External Email - Use Caution Hi, Could you please send me the password for unzipping the Freesurfer virtual machine image? Thank you and best regards, Jochen Ditterich --------------------------------------------------- Jochen Ditterich, Ph.D. Professor Center for Neuroscience Dept. of Neurobiology, Physiology & Behavior Co-Director, Center for Neuroengineering & Medicine University of California 1544 Newton Court Davis, CA 95618 USA office: +1 (530) 754-5084 lab: +1 (530) 754-6987 fax: +1 (530) 757-8827

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Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS
by fsbuild 16 Aug '23

16 Aug '23

External Email - Use Caution Hello Praise, This post, https://secure-web.cisco.com/13ufO8OPW7q_Ihf7Z4dQTf5tWtAWOGypFw1c5438ElaNLx… - indicates it is from a permission problem with _apt on the system (which may have been an Ubuntu bug/issue).    One of the more innocuous fixes suggested there is to down protect or “chmod 777” the .deb package and then try to install it.  Other fixes involve changing the permissions of system files.  I have not seen that error testing the install in a newly made Ubuntu 22 docker container. - R. On Aug 15, 2023, at 10:43, Praise Matsekete <MTSPRA001(a)myuct.ac.za> wrote: Download is performed unsandboxed as root

2 2

recon-all error
by Rosalia Dacosta Aguayo 16 Aug '23

16 Aug '23

External Email - Use Caution Dear Freesurfer team, I got the following error message after running recon-all -autorecon-pial -subjid sub-073_ses-BSL SUBJECT sub-073_ses-BSL DATE Wed 16 Aug 10:35:09 CEST 2023 USER rosalia HOST rosalia-Lenovo-Y520-15IKBN PROCESSOR x86_64 OS Linux Linux rosalia-Lenovo-Y520-15IKBN 5.19.0-45-generic #46~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 7 15:06:04 UTC 20 x86_64 x86_64 x86_64 GNU/Linux 7.3.1 (freesurfer-linux-ubuntu20_x86_64-7.3.1-20220723-115e466) /home/rosalia/software/freesurfer/bin/recon-all PWD /home/rosalia/Desktop/CAN_RUTI/sub-073_ses-BSL/mri CMD mri_brainvol_stats sub-073_ses-BSL I attach the recon-all.log file for inspection. It seems the problem is with: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 i was having troubles with the skull-stripping of this subject and what I did, and other times worked for me just fine, is run fsl_anat to skull-strip the image and then: mri_convert T1_biascorr_brain.nii.gz brainmask.mgz I replaced the problematic brainmask for this new one and ran the command above. It seems it has problems running it without troubles. Before this, I tried watershed modifying it with different "h" and also gcut and nothing seemed to work improving the skull stripping. I wonder if you could help me with this one subject. Thank you in advance for all your help. Kind regards, Rosie

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