Freesurfer

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5 participants
30076 discussions

Oracle VM - SSH
by Zoe O'Brien-Moran 09 Mar '22

09 Mar '22

External Email - Use Caution Hello FS experts I'm using freesurfer with the oracle VM and I need to SSH in from my host machine, I see that openSSH is installed on the VM, but haven't been able to get in. Does anyone have experience with/ advice for this? Thanks in advance Zoë

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Cutting the Full Surface
by Francesca Strappini 09 Mar '22

09 Mar '22

External Email - Use Caution Dear FreeSurfer experts, I'm trying to cut and flatten the full surface. I understand that tksurfer is deprecated and on my PC does not work properly. Is there an alternative way to perform the cuts? Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strappini(a)uniroma1.it <francescastrappini.stud(a)uniroma1.it>

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Using T1 FLAWS in recon-all
by Mathilde Pichon 09 Mar '22

09 Mar '22

External Email - Use Caution Hello, I know T1 MPRAGE is the prefered format to perform a recon-all segmentation. But some of my patients' data only have FLAWS images and no MPRAGE images. So is it possible to perform a recon-all with FLAWS images ? Regards, Mathilde

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ERROR: Flag -sveres unrecognized
by CALLACHAND Muntasir 09 Mar '22

09 Mar '22

External Email - Use Caution Hi, I have a problem when i try to run the function selxavg-sess<https://secure-web.cisco.com/1snqhzGaC-QpszU2KOda0ORr2TBaYIxDby42s9Iwaqfwu6…> with the optional arguments -sveres. This message occur : ERROR: Flag -sveres unrecognized Do you know what i can do to fix this? Best, Muntasir CALLACHAND

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bbregister dependencies recon-all
by Guillem París 09 Mar '22

09 Mar '22

External Email - Use Caution Hello, I'm trying to run a Boundary-based registration by using bbregister. In the documentation, it is specified that the anatomical image has to be previously analysed in FreeSurfer. I assume that means to run the "recon-all" pipeline. Now, are all the stages of "recon-all -all" needed to perform this registration? Since I am time-constrained, I would like to run as few stages as possible, so I can use bbregister. If it matters, I'm trying to register a DWI to the same subject's T1-w. Thank you! Guillem

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Error: inputs cannot have multiple frames
by HYE JUNG YOUN 09 Mar '22

09 Mar '22

External Email - Use Caution Dear Freesurfer developers, I realised some of my recon-alls been processed with the following error: ERROR: input(s) cannot have multiple frames! /Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames (I have attached the recon-all.log) I checked the mri info and I think the problem is the dimensions which is 256 x 256 x 211 x 2. I'll attach the original commands I used with mri info in txt file in case it would help you to see where I went wrong. If anyone has been through this problem or if you know what I can do to fix this, please let me know. Best, H

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Re: [Freesurfer] GLM analysis - volume and surface area
by Laura Willers de Souza 09 Mar '22

09 Mar '22

External Email - Use Caution Sorry about that! I'm resending with previous emails. The first message below is the one you didn't know how to respond to because you didn't have the previous e-mails. --------------------------------------------------------------------------------------- On 2/22/2022 9:15 AM, Laura Willers de Souza wrote: Thanks so much for the explanation! There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons. ------------------------------------------------------------------------------ On 2/21/2022 15:20 PM, Douglas N. Greve wrote: Yes, it is. It is confusing when you talk about area and volume since these are not point measures like thickness (ie, what is the volume or area of a vertex?). The area of a vertex is computed as the mean of the adjacent triangles of the vertex. The volume is the mean of the neighboring truncated tetrahedra. When you run mris_preproc, it will apply a jacobian correction (like VBM). Otherwise, it operates the same as if you had a thickness value at the vertex, ie, same GLM, etc. Make sure to use permutation for correction of multiple comparisons. ----------------------------------------------------------------------------------------- On 2/21/2022 12:13 PM, Laura Willers de Souza wrote: Hello FreeSurfer Developers, I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!? In several mailing list questions I have already seen instructions for performing these types of analysis. But I understand that freesurfer does vertex-wise analysis in the 2D surface space. So, it is not clear to me how it is possible to evaluate a 3D measurement, as volume, with a 2D method!? I've also read that surface area analysis via vertex-wise analysis doesn't make much sense. The best would be to do ROI-based analysis. Can you explain that to me? Thanks in advance! Best, Laura.

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check recon-all errors
by REEM ABU BAKR BAHATHIQ 09 Mar '22

09 Mar '22

External Email - Use Caution Hello Freesurfer experts I ran the full Recon-all pipeline on my 400 .scans data. I wanted to get the "wmparc.mgz" image of each subject. But I couldn't find it in some of them !! Where can I find the error file for the subject, as I think the process is not completed here? I would also like to inquire about the way to restart Recon-all from where the pre-processing stopped. How can I determine which step stopped processing and what should I write from a command in Linux to complete the processing process? The attached picture shows the processing output for the subject that I think something went wrong with it Thanks in advance [image: image.png]

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Permission denied error from -localGI
by Billah, Tashrif 09 Mar '22

09 Mar '22

Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 >> reading filled volume... /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading ERROR: loading /path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file '/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022 ``` Our MATLAB environment is properly setup and we regularly run other FreeSurfer-MATLAB commands. So I do not think that is causing the issue. Best, Tashrif

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hypothalamic nuclei question
by Niels Janssen 09 Mar '22

09 Mar '22

External Email - Use Caution I am trying to run the hypothalamic subunits segmentation but I am getting an error message (see below). I have FS7.2 installed on Ubuntu 18.04 (hippocampal and thalamic nuclei work fine). This error occurs even after changing the voxel size to 1x1x1 as per the instructions (because this is HCP data with 0.7mm). Thanks for your help Niels --------------- nielsj@vein:/ImageData/DataSets/HCP/3T/100206/T1w$ mri_segment_hypothalamic_subunits --i T1w_acpc_dc_restore_1mm.nii.gz --o test using 1 thread processing 1/1 Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 1463, in <module> main() File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 90, in main threads=args.threads File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 164, in predict net = build_model(path_model, model_input_shape, len(label_list)) File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 577, in build_model input_model=None) File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 750, in unet input_model=enc_model) File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 948, in conv_dec last_tensor = keras.layers.concatenate([cat_tensor, last_tensor], axis=ndims + 1, name=name) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py", line 931, in concatenate return Concatenate(axis=axis, **kwargs)(inputs) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 952, in __call__ input_list) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 1091, in _functional_construction_call inputs, input_masks, args, kwargs) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 822, in _keras_tensor_symbolic_call return self._infer_output_signature(inputs, args, kwargs, input_masks) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 862, in _infer_output_signature self._maybe_build(inputs) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 2710, in _maybe_build self.build(input_shapes) # pylint:disable=not-callable File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/utils/tf_utils.py", line 272, in wrapper output_shape = fn(instance, input_shape) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py", line 519, in build raise ValueError(err_msg) ValueError: A `Concatenate` layer requires inputs with matching shapes except for the concat axis. Got inputs shapes: [(None, 176, 184, 176, 24), (None, 48, 184, 176, 480)] -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://secure-web.cisco.com/1k8Xn2D4J0byFyRwIbmBKVyMDjJThmhtuWNmuBVgygLkSV…

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