Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

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]

3 6

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…

2 1

Linear mixed model for longitudinal data
by Julian Macoveanu 09 Mar '22

09 Mar '22

External Email - Use Caution (Apologies for reposting due to lack of answer) Dear all, This is my first attempt to analyze longitudinal structural data with freesurfer, and I just do my best to follow the tutorial. I have some things not clear, so any help would be appreciated. We have a longitudinal study design with 2 groups, healthy and patients who were scanned at baseline a second time following a variable time interval (6 to 36 months). We want to investigate whether the patient’s cortical thickness/volume progresses differently compared to controls (group-by-time interaction effects). I chose to analyze the data with LME due to variable follow-up time, having only 50% of the patients with a second scan, and also having family members within and between groups. Questions 1) To account for familial relationship, should I add a family ID as covariate that stays in the design matrix X and count this covariate as random effect when the model is fitted? Like this: lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); Where the first 3 covariates in X are counted as random effects: 1 the intercept, 2 follow-up time and 3 family ID. The X would further include group, age, sex, TIV, and group*time, the last one being the interaction term we want to assess using CM.C = [0 0 0 0 0 0 0 1]. Does the X and CM look good to address our research question? 2) It is unclear to me how to perform correction for multiple comparisons and assess what is significant. I follow this procedure after constructing X: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex,3); [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95); lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere); F_lhstats = lme_mass_F(lhstats,CM); dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0): The dvtx is not empty but has 1 value. What I don’t understand, when constructing the sig.mgh map it appears the FDR2 correction info is not used: fs_write_fstats(F_lhstats,mri,'sig.mgh','sig'); How can I be sure when I import sig.mgh in Freeview I only look at the vertexes surviving multiple comparisons? The sig.mgh file shows a lot of regions when thresholded at min 1.3 3) Given a few clusters showing an interaction effect which are saved as sig.mgh and overlaid on surface in freeview, how do I know (visualize) what is going on in these clusters, like which of the group means go up or down over time? (I use FS71 and tksurfer not working). Is it here that printing out and plotting the betas (of the interaction term) are useful for? 4) I have a hypothesis to find differences in prefrontal cortex, at which step would I apply a PFC mask? I have constructed a PFC.label file by adding corresponding label files. Thank you, Julian

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error messages from WSL Freesurfer running the samseg lesion module
by daedalus39＠aol.com 08 Mar '22

08 Mar '22

External Email - Use Caution Dear Experts, Having installed Freesurfer on WSL2, I was able to get the basic FS segmentation to run without error (i.e., recon-all runs just fine). However, when I tried to run_samseg (--lesion) on a pair of T1/co-registered FLAIR images, I received the following error messages Is there anything in the trace (below) that provides a clue? Particularly, I don't understand the "unknown data type ID: 10". Freesurfer accepts NiFTI files My command: run_samseg -o $SUBJECTS_DIR/T1T2-samseg-test -i o_ADNI_002_S_4654__MRI-m072.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii --pallidum-separate --lesion daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg -o $SUBJECTS_DIR/T1T2-samseg-test -i o_ADNI_002_S_4654__MRI-m072.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii --pallidum-separate --lesion Defaulting lesion mask pattern to [0, 0] 2022-03-08 16:26:09.870925: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2022-03-08 16:26:09.870964: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7-dev/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /usr/local/freesurfer/7-dev/subjects/T1T2-samseg-test input images: o_ADNI_002_S_4654__MRI-m072.nii, rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR.nii modelSpecifications: {'FreeSurferLabels': [0, 165, 258, ..... This process continues for a few hundred lines and then I see: maximalDeformation=0.0000 minLogLikelihood=-0.8762 appliedScaling: 1.0021 INFO: This is an unsigined short. Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 179, in <module> reg_only=args.reg_only File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 252, in segment initTransform=initTransform File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py", line 271, in register initTransform=initTransform File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 72, in registerAtlas self.saveResults( savePath, worldToWorldTransformMatrix, imageToImageTransformMatrix ) File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py", line 473, in saveResults inputImage = fs.Volume.read(self.imageFileName) File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/ndarray.py", line 103, in read result = bindings.vol.read(filename) ValueError: unknown MRI data type ID: 10 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$

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Hippocampal segmentation Matlab crash
by Caitlin R Bowman 08 Mar '22

08 Mar '22

External Email - Use Caution Hello, I am trying to run the hippocampal segmentation used in freesurfer 7. I have tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am running on a computing cluster, not locally. The same code works fine on my local computer. The managers of the computing cluster have tried to help but are stuck themselves. Find the command that I run below followed by the full error log. Best, Cait Command: segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0 Error log: ------------------------------ USER bowman2 HOST compute-081.mortimer PROCESSID 11325 PROCESSOR x86_64 OS Linux Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib ------------------------------------------------------------------------ std::terminate() detected at Thu Feb 24 14:14:37 2022 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Default Encoding : UTF-8 GNU C Library : 2.17 stable MATLAB Architecture: glnxa64 MATLAB Root : /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 Processor ID : x86 Family 6 Model 63 Stepping 2, GenuineIntel Fault Count: 1 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00002baa657204e8 RCX = 0000000000000000 RDX = 00002baa6570f758 RSP = 00002baa93ffb0b0 RBP = 00002baa93ffb470 RSI = 00002baa654c3fb3 RDI = 00002baa93ffb0c0 R8 = 0000000000000000 R9 = 00002baa60271f90 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 00002baa65730520 R13 = 00002baa93ffc0b0 R14 = 00002baa93ffc090 R15 = 00002baa93ffc470 RIP = 00002baa65422f4e EFL = 0000000000000000 CS = 0000 FS = 0000 GS = 0000 Stack Trace (captured): [ 0] 0x00002baa65422f4e /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478 _ZN2fl4diag5linux12context_base12capture_dataEv+00000030 [ 1] 0x00002baa65420424 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428 [ 2] 0x00002baa740ef0f5 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597 [ 3] 0x00002baa740f12ca /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258 [ 4] 0x00002baa740f13c1 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505 [ 5] 0x00002baa740f1743 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403 [ 6] 0x00002baa740f17b3 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515 [ 7] 0x00002baa5ffe4a06 /lib64/libstdc++.so.6+00387590 [ 8] 0x00002baa5ffe4a33 /lib64/libstdc++.so.6+00387635 [ 9] 0x00002baa5ffe4c53 /lib64/libstdc++.so.6+00388179 [ 10] 0x00002baa60fe3822 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00325666 _ZN2fl4i18n14MessageCatalog17GetMessageCatalogERKNS0_9CatalogIDERKNS0_8MwLocaleE+00001186 [ 11] 0x00002baa60fe4113 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00327955 _ZN2fl4i18n14MessageCatalog11get_messageERKN13resource_core9BaseMsgIDERKNS0_8MwLocaleE+00000051 [ 12] 0x00002baa6589bf57 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01482583 [ 13] 0x00002baa6589ae6f /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01478255 [ 14] 0x00002baa65832a44 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmx.so+01051204 _Z14mxWarningMsgIdRKN13resource_core9BaseMsgIDE+00000052 [ 15] 0x00002baa74443a95 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01100437 [ 16] 0x00002baa74443d2f /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwjmi.so+01101103 _Z50mljInitFirstCrackSignalHandlerIfJavaAlreadyStartedv+00000015 [ 17] 0x00002baa740c5855 /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00698453 [ 18] 0x00002baa740b64ec /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00636140 [ 19] 0x00002baa740a2cdd /raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00556253 [ 20] 0x00002baa607adea5 /lib64/libpthread.so.0+00032421 [ 21] 0x00002baa60ac0b0d /lib64/libc.so.6+01043213 clone+00000109 If this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1RD2fc7k7E8B1e1GuwRGzMU8V8DVzFuosUwM0pYlETnQWtE… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /home/bowman2/matlab_crash_dump.11396-1 ** MATLAB is exiting because of fatal error /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/run_segmentSubjectT2_autoEstimateAlveusML.sh: line 40: 11396 Killed /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/segmentSubjectT2_autoEstimateAlveusML sub-CC110037 /home/bowman2/Data/camcan/fs_camcan/ /raid-18/LS/bowman2/camcan/imaging/anat/sub-CC110037/sub-CC110037_T2w.nii.gz 0.333333333333333333333333333333333333 /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 T2 '/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/fs_run_from_mcr /sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/bin/' 0 1 0 @#@FSTIME 2022:02:24:14:14:35 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 e 1.65 S 0.13 U 1.19 P 80% M 67608 F 0 R 19447 W 0 c 32 w 559 I 0 O 84720 L 5.00 5.06 4.81 @#@FSLOADPOST 2022:02:24:14:14:37 run_segmentSubjectT2_autoEstimateAlveusML.sh N 18 5.00 5.06 4.81 Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Thu Feb 24 14:14:37 CST 2022 -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee

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Question about editing topology errors
by Trisanna Sprung-Much 08 Mar '22

08 Mar '22

External Email - Use Caution Hi there I have this issue occurring in several hemispheres (See images attached) where a “sulcus” is created because the pial crosses where it shouldn’t, and am wondering what the best way to edit this is. I don’t think it is a matter of adding WM control points as it is not the WM that needs to be corrected but rather the pial. My 2nd image shows how the sulci should look in the pial. Should it be just a matter of removing voxels in the brainmask.mgz and doing recon-all -autorecon-pial -subjid I tried this for one subject and it was not happy. Is there a way to add control points for the pial? Thank you! Trisanna Sprung-Much, PhD McGill University Montreal Neurological Institute --

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Re: [Freesurfer] password for virtual machine
by fsbuild 07 Mar '22

07 Mar '22

External Email - Use Caution Hello Xavier, Sending the into to your email shortly. - R. On Mar 7, 2022, at 17:32, Xavier Caldú Ferrús <xcaldu(a)gmail.com> wrote:        External Email - Use Caution        Dear all,I have just downloaded the virtual machine + ubuntu package and I need the password to log in. Would you be so kind as to send it to me?Thank you very much.Best,Xavier_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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password for virtual machine
by Xavier Caldú Ferrús 07 Mar '22

07 Mar '22

External Email - Use Caution Dear all, I have just downloaded the virtual machine + ubuntu package and I need the password to log in. Would you be so kind as to send it to me? Thank you very much. Best, Xavier

1 0

Co-registration without ant resolution cost
by Salar Dini, Elaheh 07 Mar '22

07 Mar '22

External Email - Use Caution Dear Freesurfer developers, I have a dwi.nii image which I want to co-register on a orig.mgz (produced by running recon-all on the subject's T1 image) file without any drop in the quality of image (i.e. without any resolution cost, or changes in the acquired dwi intensity at each voxel). I was told that if you just translate the image and don't rotate it during co-registration, the quality of the image won't drop, because you don't cut through the existing voxels on the original image in resampling process to fit it in the destination image. Also, I'm not sure if the --no-resample flag in mri_vol2vol helps with that. Can you please guide me toward a better understanding of how co-registration affect the image quality? and ways to prevent that? Freesurfer version: 7.2 & the Platform in use: CentOS7 Thank you and all the best, Ela

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Freesurfer March 2022