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30070 discussions

EPI Factor generated by dmri_bids_config
by Blujus, Jenna 27 Jun '23

27 Jun '23

External Email - Use Caution Hi all, I am using TRACULA (v7.3.2) to examine longitudinal changes in WM integrity by diagnostic groups. For preprocessing, I did not use topup because my data have a single acquisition (i.e., I do not have two acquisitions with opposing polarities of the phase-encode blips). But I did utilize the Eddy command for eddy current and motion correction. To do so TRACULA requires information regarding the epi factor, echo spacing, and phase encoding direction. My data are in BIDS format and so I used the dmri_bids_config script to extract these factors. While the echo spacing and PE direction match the information in my json files, I am finding that I am getting a large EPI factor (e.g., 115001.0273). I looked at the acqp.txt file generated for use with Eddy and the correct values are stored in the file for each subject (PE direction [0 1 0] and total readout time) so I believe the command was executed properly despite the large magnitude EPI factor. My questions are: 1. How is the EPI factor used in preprocessing by TRACULA? 2. Will the magnitude difference in the EPI factor affect the preprocessing of the DWI data if topup is turned off and only eddy is used? Thanks, Jenna

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Re: [Freesurfer] FS_7_2_0_ubuntu_198_04_06 root password
by fsbuild 27 Jun '23

27 Jun '23

External Email - Use Caution You were already sent the login credentials. If you have unzipped the archive, setup and started the VM and successfully logged in as the user shown in the login screen, then you can run system commands via "sudo".  No other login is needed to run Freesurfer in the VM.   We don't support otherwise modifying the VM, setting up other userids, etc. - R. On Jun 27, 2023, at 02:58, marco.muti(a)tin.it wrote:        External Email - Use Caution        Would you please send me the root password for FS_7_2_0_ubuntu_18_04_06?   Thanks!!! _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Missing file colortable_BA_thresh.txt for recon-all-clinical
by Michael Mc Laughlin 27 Jun '23

27 Jun '23

External Email - Use Caution I finally was able to run recon-all-clinical.sh without errors! There is a file in the development fork on Github called *colortable_BA_thresh.txt* in the *average* directory that is not present in the 7.4.1 release. When I downloaded this and put it into the 7.4.1 release, the replacement recon-all-clinical.sh ran without any errors. I also solved the mystery of the missing lateral ventricles. The file mri/brainmsk.mgz in the clinical version is a synthetic file that doesn't contain any ventricles. The equivalent to brainmsk.mgz in the clinical version is synthSR.mgz. This has the missing ventricles and indeed all the other brain components like the cerebellum etc. Alas, despite running error free, there is still no stats/aseg.stats file. I hope that this is on the TODO list for the developers. In the meantime I will write a matlab function to extract the aseg stats from mri/aseg.mgz, which seems to have all the necessary data. If anyone wants a copy of this please email me. Michael McLaughlin,

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removal
by Pavlina.Pokosova＠fnmotol.cz 27 Jun '23

27 Jun '23

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FS_7_2_0_ubuntu_198_04_06.ova unzip password
by marco.muti＠tin.it 27 Jun '23

27 Jun '23

External Email - Use Caution Would you please send me the unzip pass for FS_7_2_0_ubuntu_198_04_06.ova? Thanks!

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F mgh file
by Adriana Cannizzaro 26 Jun '23

26 Jun '23

External Email - Use Caution Dear FreeSurfer team, We would like to extract the F value from the group effect. Based on previous posts, we should use the file F.mgh in order to achieve that. How can this method be used without a matlab licence ? Is there any possibility to start a matlab terminal using FreeSurfer's matlab libraries ? Thank you in advance ! Adriana Cannizzaro

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Ubuntu unzip password request
by 朱宣龙 26 Jun '23

26 Jun '23

External Email - Use Caution Hi, I am attempting to install Ubuntu following the tutorial provided on the wiki, but it requires a passcode to open the image. Can I ask for the password for the FS_7_2_0_ubuntu_18_04_06.ova.7z? Thanks. Best, Xuanlong

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Passcode for Archive
by James 25 Jun '23

25 Jun '23

External Email - Use Caution Hello Could I please receive the password for the "FS_7_2_0_Ubuntu_18_04_06.ova.7z" archive found on this webpage? VM_67 - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1E92JsdZSI1gtiuORgMd2oCcSlY4i2MfgunlqfmHQmaxG2…> Thank you for your time, James Watlington <http://secure-web.cisco.com/1JMdry0mYYRqdCZXgCAgpYd6amucC9yr_uIRr2AOKt91e2y…> Virus-free.http://secure-web.cisco.com/150KFIPXTYGg8PLLzxh2AyFWzWp-y2aUN3mF… <http://secure-web.cisco.com/1JMdry0mYYRqdCZXgCAgpYd6amucC9yr_uIRr2AOKt91e2y…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Troubleshooting "could not open file" errors in FS 5.3
by Annchen Knodt 24 Jun '23

24 Jun '23

External Email - Use Caution Hello, I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past. On my first pass, I attempted to run this full recon-all command: /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz And eventually got the error: MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using: /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh And eventually got the error: MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking) Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8): $ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp --- > ln -s $subj1 ${diffsubj}_tmp 3753c3753 < cp $subj1 ${diffsubj}_tmp --- > ln -s $subj1 ${diffsubj}_tmp 3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) --- > set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage) 4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) --- > set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage) 4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) --- > set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average) Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!! Annchen

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'ValueError: numpy.ndarray size changed...' in mri_synthseg&synthstrip (numpy1.20.3)
by Mu Nan 24 Jun '23

24 Jun '23

External Email - Use Caution Dear FreeSurfer experts, I have recently upgraded to the latest stable version, 7.4.1, in order to try out the new features of SynthSeg and SynthStrip. However, I have encountered some errors. My laptop's chip is M2. Could someone please provide some guidance? Initially, I was able to run mri_synthstrip, but not the mri_synthreg. I got the error message as: (base) MacBook-Pro-M2:$ mri_synthseg -i ./mci_test/mri/orig.mgz -o ./mci_test/ai_test --threads 8 Traceback (most recent call last): File "/Applications/freesurfer/7.4.1/python/scripts/mri_synthseg", line 10, in <module> import surfa as sf File "/Applications/freesurfer/7.4.1/python/lib/python3.8/site-packages/surfa/__init__.py", line 19, in <module> from .image import Volume File "/Applications/freesurfer/7.4.1/python/lib/python3.8/site-packages/surfa/image/__init__.py", line 1, in <module> from .framed import FramedImage File "/Applications/freesurfer/7.4.1/python/lib/python3.8/site-packages/surfa/image/framed.py", line 24, in <module> from surfa.image.interp import interpolate File "surfa/image/interp.pyx", line 1, in init surfa.image.interp ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject Enlightened by #msg74713 and #msg73091, I upgraded the numpy version from 1.19 to 1.20.3, and also installed a python specific for M1/M2. $ sudo /Applications/freesurfer/dev/python/bin/python3 -m pip install numpy==1.20.3 (I couldn't use $ sudo fspython -m pip install, because it said my freesurfer is not properly sources, which is weird since I am sure it was sourced in a right way. But now both mri_synthseg and mri_synthstrip can't run. Now if I enter the commands $ fspython -m pip freeze, the outputs are: ... neurite==0.2 nibabel==5.1.0 numpy==1.20.3 oauthlib==3.2.2 opencv-python==4.7.0.72 ... tensorboard==2.11.2 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.1 tensorflow @ file:///Users/mu/Desktop/tensorflow-2.4.1-py3-none-any.whl tensorflow-estimator==2.4.0 tensorflow-io-gcs-filesystem==0.32.0 Best, Mu

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