Re: [Koha-devel] Carrousel display issue on sandbox

the static files, which is, I think, the way to go for plugins. Is this a regression you noticed recently or you are developing a new version of the plugin? Le lun. 11 sept. 2023 à 21:10, Shi Yao Wang a écrit : Hello, Our carrousel plugin display is broken on koha sandbox and it&#x

Re: [Koha-devel] Carrousel display issue on sandbox

the other plugin developers could help? Katrin On 12.09.23 08:44, Fridolin SOMERS wrote: Oooo I did not knew the repos of InLibro have moved. Great :) I suggest you add topic koha-plugin on those repos : https://github.com/topics/koha-plugin Best regards, Le 11/09/2023 à 09:32, Shi Yao Wa

Re: [Koha-devel] Carrousel display issue on sandbox

Hello, here it is: https://github.com/inLibro/koha-plugin-carrousel Shi Yao On 2023-09-11 15:26, Katrin Fischer wrote: Hi, sorry, I should have been more clear: Can you post the link to the repository? Katrin On 11.09.23 21:22, Shi Yao Wang wrote: version 4.1.4 On 2023-09-11 15:13

Re: [Koha-devel] Carrousel display issue on sandbox

version 4.1.4 On 2023-09-11 15:13, Katrin Fischer wrote: Hi Shi Yao, as there are multiple versions of the carousel plugin around, which one did you use/install? Hope this helps, Katrin On 11.09.23 21:10, Shi Yao Wang wrote: Hello, Our carrousel plugin display is broken on koha sandbox

[Koha-devel] Carrousel display issue on sandbox

Hello, Our carrousel plugin display is broken on koha sandbox and it's due to the plugin's js/image files not being found (on webpage inspect console). Tested this on 2 sandboxes with the exact same errors. Any idea how this could be fixed on the sandboxes? Thanks, Sh

[Freesurfer] Job opening: Full/Part-time medical imaging scientist: PWI/DWI/ASL/SWI

External Email - Use Caution Dear list members, Please check the attached job ad for a medical imaging scientist position at Atlanta, GA. We need experts for medical imaging analysis, especially for PWI, DWI/DTI, ASL or SWI. The position could be part-time and projected based.

[Freesurfer] Deep Learning Scientist for Medical Imaging

External Email - Use Caution Deep learning Scientist for Medical Imaging YIWEI Medical Inc. www.drbrain.net Locations: Atlanta, GA, USA / Shenzhen, China We are looking for talented, driven and autonomous candidates who are professional for deep learning develop for medical i

[Freesurfer] Can I use FS to detect white matter lesion using FLARE imaging?

Dear FS experts: Can I use FS to detect white matter lesion using FLARE imaging? Where can I find the command. Thanks Lawrence Radiology Department Emory University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] Correcting defect

Dear FS experts, I am running FS 6.0. There is a error message like this. [image: Inline image 1] are there any way to modify it? thanks Lawrence Radiology Department Emory University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] automatic quality control in freesurfer

Dear FS experts: Just wondering if there were any automatic method to perform quality control especially for segmentation. thanks Lawrence ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

[Freesurfer] do I need to re-ROI the segmentation after recon-all

Dear FS experts: After I finishing recon-all, do I need to check the segmentation and re-roi some of region? thanks Lawrence Emory University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

[Freesurfer] Convert mgz figure

Dear FS expert, Is that possible to extract .jpg or .tiff files by using command line? Or convert .mgz file to other format file? If ok , then I can write a program to do this action automatically. Thanks Lawrence ___ Freesurfer mailing list Freesurfer@

[Freesurfer] ADNI longitudinal brain volume in normal subjects

We are working on a longitudinal study for brain volume compartment in the specific population. I am wondering if there are any longitudinal brain volume data for normal patients? I saw some studies using ADNI normal data as reference, but cannot find them. thanks! Lawrence Emory University __

[Freesurfer] neither NIfTI-1 qform or sform are valid

Dear FS experts: There are some error message when I running recon-all as following: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented Are there any problem in raw data? I am using MRICRON to convert DICOM to nii thanks Lawrence __

[Freesurfer] Can I use specific template for FS computing

Dear FS experts: We generated a specific population of brain template. Just wondering if FS can use these templates to measure brain volume. thanks Lawrence Emory ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.ed

[Freesurfer] freesurferstats2table_bash

Dear FS experts: Would you pls provide freesurferstats2table_bash script? The link of http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table does not work. thanks Shiyao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] summary 500 samples FS results

Dear FS expert, We have running around 500 samples by FS. I am wondering if there are easy way to summary these data. i.e., generate mean of cortical thickness. thanks Shiyao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

[Freesurfer] How can I get cerebral WM and cortex volume

Dear FS experts: How can I get the whole cerebral WM and cortex volume. I am using following command: asegstats2table --subjects 10001 --segno 2 3 41 42 24 --tablefile 10001_WB_table It shows that no 2,3, 41,42 segment NO, however, they can be found in the FreeSurferColorLUT.txt file. thanks L

[Freesurfer] measuring basal ganglia volume

Dear FS experts: We are measuring population based basal ganglia volume. Except the absolute volume of BS, any other parameters could be a reliable marker to reflect BS volume? such as ratio of total subcortical GM volume. Thanks! Lawrence ___ Freesurfer

[Freesurfer] Error in aparcstats2table

Dear FS experts: I am using aparcstats2table command to generate mean thickness of group subjects. my commands: aparcstats2table --subjects 10002 10003 10004 --hemi lh --meas thickness --tablefile aparc_stats_LH.txt 10002, 10003, 10004 are subjects. However, there were error message as: "File "

[Freesurfer] Freesurfer for PET images

Dear FS experts: We have a few PET images for brain. Just wondering if FS can be used to measure brain volume? Do I have to have T1 MRI as reference? thanks Lawrence ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] How to check if FS are processing correctly.

Dear FS experts: I am using FS to analyze our MRI data. When I finished recon -all, there are following informaion: Started at Fri Mar 10 11:26:05 EST 2017 Ended at Fri Mar 10 18:26:51 EST 2017 #@#%# recon-all-run-time-hours 7.013 recon-all -s 10001 finished without error at Fri Mar 10 18:26:51

[Freesurfer] MRI intensity normalize

Dear FS experts, I am wondering the process of MRI intensity normalization. Before I am running recon -all, can I run following process to normalize our MRI images. mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm or any other preprocessing methods to avoid bias. thanks Lawrence Emory University

[Freesurfer] how to export cortical thickness in to .txt

Dear Fs experts: I would like to use mris_anatomical_stats to calculate 35 cortical regions thickness. I am using following command: mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] how to export cortical thickness in to .txt

Sorry for the interrupted. My question is how to export the results to .txt files. I found that there is a -f argument, however it doesnot work. thanks Shiyao On Fri, Feb 3, 2017 at 11:41 AM, shi yao wang wrote: > Dear Fs experts: > I would like to use mris_anatomical_stats to calcul

[Freesurfer] Cannot find CTF archive

Dear FS experts: when I running hippocampus subfield, I got error messages:" Cannot find CTF archive". I copied command and screen to you. Thank you very much! [silun.wang@node5 N01]$ *recon-all -s N01 -hippocampal-subfields-T1* Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6

[Freesurfer] How to check recon-all finished without any error

Dear FS experts: How to check recon-all finished without any error? Sometime, there are showing no error message, however, when I running hippocampus subfield, it does not run. thanks Lawrence Emory ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] Error message

Dear FS teams: when I running FS, there is a message like this: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf Is it a real Error message? Cause, it seems that the recon -all process successfully finished. thanks Lawrence ___

[Freesurfer] Using other brain template to calculate cortical thickness

Dear Douglas Thank you so much for your reply!! Another question: Can we use other brain template to calculate cortical thickness? If yes, How can I do it. thanks Lawrence ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.h

[Freesurfer] aseg.stats data output

Dear FS experts: How can I only out put the volume value in the aseg.stats file? I applied following command: but it will produce a table with lots of values such as brainsegvol, brainsegvolnotvent, which I donot want to use. thanks asegstats2table --subjects 004 021 040 067 080 092 \ --segno

[Freesurfer] query about the "normal range" in aseg.stats

Dear FS experts: I noticed that there is a "normal Range" results in the aseg.stats table. I am wondering how can I consider of this normal range? is that based on population or what. thanks Lawrence Emory University ___ Freesurfer mailing list Freesurf

[Freesurfer] Factors affect cortical thickness in normal population

Dear FS experts, We have few dataset of normal patients. They will be arranges as controls. I am wondering the factors affecting normal patients cortical thickness: Age, Sex Native Language Hand prefer IQ Any others? thanks Lawrence ___ Freesurfer maili

[Freesurfer] tcsh update

Dear FS experts: I am running FS in local computer and showing following error message and program stopped at recon-all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Do I need to update tcsh? and how can I do it. thanks Lawrence ___

[Freesurfer] qdec error

Dear FS experts: I am trying to qdec to analysis FS results. when I loading qdec.table.dat, it shows cannot open the data (could not fine column name of fsid or ID) Following is my qdec files: /home/Lawrence/Lawrence_data fsid Gender age diagnosis L_frontal_V L_cingulate_V L_occipital_V L_tempor

[Freesurfer] MRI image prepossession for FS

Dear FS experts, I am planning to use FS to analyze large dataset from population. I am wondering if there were software can automatically check T1 imaging quality for FS? such as monitoring head motion, noise, et al. thanks Lawrence Emory ___ Freesurfe

[Freesurfer] fs development version

Dear Experts: I set up FS development version. And now it shows error message: -- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please

[Freesurfer] Brainstem Substructures does not work.

Dear FSL expert: Firstly, I would like to thank for the reply from Douglas. Thank you for your suggestion! aparcstats2table is working!. Then, I have another question about the brainstem substructures. According to the guideline, https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime I download t

[Freesurfer] Command to summarize 35 cortical thickness

Dear FS expert, I am using command "mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh" to calculate cortical thickness in 35 regions. I have 50 subjects. I am wondering how can I summarize these results and export to one document? (I just need cortical thickness results) thanks L

[Freesurfer] Build fsaverage

Hello, Thank you very much for the reply! 1. I copied calculated data into a new computer and I cannot find "fsaverage". 2. Bruce, thank you! I used make_average_subject command. However, it shows that error message: "lack of memory". I am wondering how can I do that. Thank you for helps again!

[Freesurfer] build fsaverage

Hello ! I work for the department of radiology, Emory University. We're planning to use the FreeSurfer software suite (or more precisely, the surface-based stream ) in a project that aims to compare cortical thickness between treatment and nontreatment patients. We have finished recon-all for al

[Freesurfer] Increase VBOX disksize

Dear Sir/Madam I am using freesurfer to proceeding brain MRI data. I have 30 cases. However, the space for home is no enough. I am wondering how can I increase disk space to computing my data. I use Vbox unbentu system. thanks Lawrence ___ Freesurfer mai