Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

Questions about the different ways in which metrics such as the cortical surface area can be extracted in Freesurfer
by 1500787798 20 Aug '23

20 Aug '23

External Email - Use Caution Dear FreeSurfer developers,            The surface area in fsaverage space that I extracted with the first command below is not the same as the value under the same DK brain region extracted from the lh.parc.stats file generated as a result of preprocessing with the second command. I summed or averaged the surface area of the vertices of the corresponding brain region under the fsaverage space, and the result is still not the same as the one presented directly under the stats file, and I would like to know why this is the case? 1. mri_surf2surf --srcsubject $subject --sval area.pial --src_type curv \   --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/$subject/lh.area.pial.fsaverage.mgh --trg_type curv --hemi lh 2. aparcstats2table --subjects $subject --hemi lh --parc aparc --meas area --tablefile lh.area.txt       Best, Jinfeng Hou

2 1

Re: [Freesurfer] ScLimbic issue
by fsbuild 20 Aug '23

20 Aug '23

External Email - Use Caution Please let us know what FREESURFER_HOME is set to, and what (Linux or Mac) operating system your machine is running.  If you are on a Mac please indicate if it is one of the current silicon Macs (M1, M2, chip) or one of the older Intel Macs. - R. On Aug 20, 2023, at 14:57, Jacobs, Heidi I.,PHD <HJACOBS(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Hello FreeSurfer team, I am trying to run the sclimbic tool on our FreeSurfer processed images (from the Martinos center).For some unknown reason I keep getting the same problem:Excluding seg [853]Using CPUIllegal instruction (core dumped) Not sure what this means?I have sourced /usr/local/freesurfer/nmr-dev-env  and set the SUBJECTS_DIR correctly.I tried with the - - s option referring to the FreeSurfer processed subject as well as the - - i option, referring to the orig.mgz image.Using the nifti image or the mgz image doesn’t make a difference either. Any suggestions on what the problem may be or how to resolve this? Thank youAll the bestHeidi_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Partial Correlation from mri_glmfit
by Finn, Quentin 20 Aug '23

20 Aug '23

External Email - Use Caution Freesurfer experts, I have some surface data (say thickness) that I'd like to correlate with a neuropsyche measure (so one value per subject, a continuous variable) This is complicated, though, by the presence of a (discrete) covariate that splits my cohort up into three groups (for ease of explanation, say the groups are: young, middle, old). I'm hoping to use mri_glmfit to see where the neuropsyche is a significant predictor of thickness while controlling for the group effect, but I'm struggling to set up the contrast / fsgd matrix Is there a way to accomplish this in mri_glmfit? thanks so much for your help! Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas* for 12 years in a row and recognized us on the Honor Roll seven times. For more than 100 years, we have provided patients with the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. *In a two-way tie houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

Native coordinate to MNI305 to MNI152
by Qian Chu 20 Aug '23

20 Aug '23

External Email - Use Caution Dear list, I'm working on intracranial electrode localization and am developing a pipeline to map electrode coordinates in the native RAS space to brain templates like fsaverage/MNI305 and MNI152. I would like to check whether my workflow is correct and would appreciate any input on the validity! The steps are described below: 1. Obtain electrode coordinates (in mm) on the native orig.mgz as an array [R A S] 2. Read the 4x3 matrix (tal_mat) in mri/transforms/talairach.xfm. Obtain the new coordinates in MNI305 = tal_mat * [R A S 1]' 3. Use the MNI305 to MNI152 matrix (305_152_mat) mentioned in https://secure-web.cisco.com/1KBgpyl2eUHbe3JJquLznCmUPf5H6Y6u32jsqi9JO-tyM4… (8th Use case). Obtain the new coordinates in MNI152 = 305_152_mat * [R_305 A_305 S_305 1]'. Where R/A/S_305 is the output from step 2. Thank you very much in advance! Best regards, Qian -------- QIAN CHU (he/him/his) | qian.chu(a){mail.utoronto.ca, ae.mpg.de} | Website<https://secure-web.cisco.com/1sSvt_8iF8TDt6AOi7fpFSVomBHHihzVXzlD8iQRtgls4n…> PhD Student, Max Planck - University of Toronto Centre for Neural Science and Technology - Neural Circuits, Consciousness, and Cognition Research Group<https://secure-web.cisco.com/12q0YRBUXUV2R0upgxdIxqSAdxXp93zy9YPIQn5p4K4-u8…> Max Planck Institute for Empirical Aesthetics - Neuron to Brain laboratory<http://secure-web.cisco.com/1YurU9IJfcJ0-OPOy4t2cSOIsEPbKHXN3-14v8LYQEBcrC8…> Institute of Biomedical Engineering and Krembil Brain Institute, University of Toronto

2 2

converting preprocessed surface functional data to volume
by wangzhiwei3233 20 Aug '23

20 Aug '23

External Email - Use Caution Dear Freesurfer experts, I am going to convert the preprocessed surface functional data to volume in fsaverage space so that I can used the processed data in SPM for further analysis, for example, beta series analysis. I tried mri_surf2vol, it worked. But it is time consuming. It takes around 5 minutes per 10 volumes. In addition, the result volume is too big (67MB/ volume for 256*256*256 matrix, 1mm resolution). My data contains about 70800 brain volumes, so the needed time is about 40days and the storage space is about 7TB , which is unacceptable. The code is as follows: mri_surf2vol --o ${Dir_Subj_fMRI}/$isub/bold/${irun}/Ribbon/${iVolume} --subject fsaverage --so ${SUBJECTS_DIR}/fsaverage/surf/lh.white ${Dir_Subj_fMRI}/$isub/bold/${irun}/LH/${iVolume} --so ${SUBJECTS_DIR}/fsaverage/surf/rh.white ${Dir_Subj_fMRI}/$isub/bold/${irun}/RH/${iVolume} Are there methods with faster speed and outputing volumes with lower resolution? Best, Zhiwei

2 1

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

2 1

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

2 1

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.

2 1

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

1 0

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.

2 1

← Newer
1
2
3
4
5
6
7
8
9
...
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2023