Hi,
That sounds like this issue, which we haven’t patched quite yet:
https://github.com/Washington-University/HCPpipelines/issues/119
Incidentally, you must be running off code in the current master branch, rather
than the formally tagged “v4.0.0” release
As part of some other updates to the StructuralQC scenes themselves, I recently
created a more sophisticated generation script that should use relative paths
within the scene.
Please try the just updated master branch of
https://github.com/Washington-University/StructuralQC
We have tested
-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Moataz Assem
Date: Tuesday, June 18, 2019 at 8:00 AM
To: "Glasser, Matthew" , "Harms, Michael"
, "hcp-users@humanconnectome.org"
Subject: RE: [HCP-Users] film_gls error pinv() s
Hmmm. Assuming the problem is reproducible, I think you’ll have to report
this, to the FSL list. To provide additional information, it might be helpful
to hack the TaskfMRILevel1.sh script to not use the ‘--sa --ms=15 --epith=5’
flags in the call to ‘film_gls’ (or, perhaps easier, just try
Hi,
I’m not sure if the new training file is ready for public release yet, but just
to clarify, to clean short fMRI runs, you really need to use multi-run FIX to
get better separation of the signal/noise components. The new training file
will help around the margins, but using MR-FIX is
Are you sure that there is duplication of actual *data* on the different
drives? Just because a subject ID appears on multiple drives doesn’t mean that
data under that subject ID is the same on the drives.
Cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
It isn’t surprising that data will be missing in some subjects, due either to
problems at the scanner, or problems during processing.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University
Try the very latest master, which should resolve this issue. (I was just
working on this 30 min ago). Please let us know if it works.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: 温景熙
Date: Thursday, May 30, 2019 at 9:24 PM
To: "Glasser, Matthew" , "Harms, Michael
South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: "Glasser, Matthew"
Date: Thursday, May 30, 2019 at 3:52 PM
To: Reza Rajimehr , "Harms, Michael" ,
Nooshin Abbasi
Cc: hcp-users
Subject: R
Hi Reza,
1) We’ve already generated Cohen’s d-style effect size maps for all contrasts,
using all subjects, as part of the “Group Average Dataset” available at
https://db.humanconnectome.org/data/projects/HCP_1200. If you need it computed
for a specific subset of subjects, then yes, you can
Hi,
All those details, including an importable VE11C protocol are available at
http://protocols.humanconnectome.org/
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
: Leonardo Tozzi
Date: Wednesday, May 29, 2019 at 1:44 PM
To: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
I did and actually some subjects worked, but not these ones: 101006 159441
926862 92735
, May 29, 2019 at 11:40 AM
To: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Dear Michael,
I have now downloaded the majority of subjects with:
curl -o …/${sub}_${run}_Movement_RelativeRMS.txt
Hmmm. What is the specific error message that you are getting? In the 4.0.0
pipelines, the necessary custom scripts that you mentioned are provided with
the pipeline distribution, and are contained in the
HCPpipelines/FreeSurfer/custom directory.
It sounds like you don’t have something
Hi,
If you simply want all the FreeSurfer quantification in tabular form, you can
select the “Expanded FreeSurfer Data” link under “Quick Downloads”, available
here https://db.humanconnectome.org/data/projects/HCP_1200
(You will need a ConnectomeDB account).
Cheers,
-MH
--
Michael Harms,
Hi,
If you want to try downloading via https://db.humanconnectome.org and Aspera,
simply select the “All Family Subjects” category under “Download Image Data”
and then select the “Diffusion” modality on the “Download Packages” page.
That will select all 1065 subjects with Diffusion data –
Hi,
The Movement_RelativeRMS.txt files aren’t part of the specific “${run}_FIX”
resource that you tried to reference.
If you have access to outputs in our standard file/directory organization
(e.g., Amazon S3, Connectome-in-a-Box, or our downloaded “packages”), the
Movement_RelativeRMS.txt
In the case of the 7T data, the 1/2/3/4 are just used to distinguish the
different resting state runs, acquired in different scan sessions. The numbers
are not intended to imply that each scan was acquired on a different day. We’d
have to look, but I suspect that 1/2 were typically acquired
While I’m not surprised that the ICCs would be lower for an anatomical-based
measure for MSMAll than MSMSulc, I am surprised by the magnitude of the change
(from 0.9 to 0.65), especially for a parcellated analysis, since only changes
in the precise border of the parcellations should be
Hi,
I suggest directing your inquiry to the FSL-Users list.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Joseph Orr
Date: Wednesday, April 24, 2019 at 10:51 AM
To: "Harms, Michael"
Cc:
Why not simply report the parcel name and its values? And consider putting the
scene on BALSA, so that others can easily access the data.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University
For users that want to follow this, please see:
https://github.com/Washington-University/HCPpipelines/issues/108
It has something to do with the fact that we needed to apply manual
reclassification of the FIX output in that particular subject/run.
Cheers,
-MH
--
Michael Harms, Ph.D.
We have seen this occur on rare occasions, and don’t have an explanation for it.
Try just running fMRIVolume again.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Hi,
We suggest you use PALM, since you need to use permutation to determine the
distribution of the TFCE metric.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department
That particular error message can be ignored. We’ll fix the scripts so that it
doesn’t occur in the future.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of
FYI: The “prediction of fluid intelligence” aspect of Finn et al (2015) has
already been extended to final HCP-YA release via a different research group in
this study:
https://www.ncbi.nlm.nih.gov/pubmed/30104429
cheers,
-MH
--
Michael Harms, Ph.D.
We extended that feature such that it should be an accepted option for all the
"ICAFIX"-related scripts, but we haven't had a chance yet to extend it to the
context of MSMAll and TaskAnalysis. Hopefully in the near future...
--
Michael Harms, Ph.D.
Sorry, but I think you are going to have to get support from Anderson and the
FSL list for this one.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
doesn't even output anything if it isn't a symlink, while the
point is to find the real location whether it is a symlink or not (because it
needs other files from that directory).
I guess I will make it test whether "$0" is a symlink first.
Tim
On Mon, Apr 1, 2019 at 9:31 AM Harms, Mic
Also, see here
https://github.com/ecr05/MSM_HOCR/issues/5
for some info from Emma.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid
Check RS_fMRI_2_hp2000.ica/.fix.log for clues. Also, what’s in the stderr
output from the run?
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660
The MR-FIX releases as part of HCPpipelines v4.0.0 should work with FSL 6.0.1.
As far as MSMAll and FSL 6.0.1, to my knowledge, we haven't explicitly tested
that combination yet.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate
8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Shachar Gal
Date: Wednesday, March 20, 2019 at 3:32 PM
To: "Harms, Michael"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-U
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Shachar Gal
Date: Wednesday, March 20, 2019 at 3:23 PM
To: "Harms, Michael"
Hi,
The FreeSurferFolder is located at $StudyFolder/$Subject/T1w/$Subject, which is
what PostFreeSurferPipeline.sh is setting up via the following combination of
lines:
FreeSurferFolder="$Subject" #L101
T1wFolder="$StudyFolder"/"$Subject"/"$T1wFolder" #L137
Running the PostFix script will generate a scene that allows you to review the
FIX classification.
Don’t recall seeing a surface contour/glitch quite like that before. It
definitely merits further investigation. E.g., what do the adjacent slices
look like? What does the actual surface look
Hi,
Sounds like a coding error. If you’ve converted your T1w and T2w scans to
proper NIFTIs, then you should be able to use those as inputs. Did you review
Examples/Scripts/PreFreeSurferPipelineBatch.sh ?
If you get it working, let us know how the myelin maps look!
Cheers,
-MH
--
Michael
/T1w/ contains all the FreeSurfer output.
So, /T1w//stats contains the usual FS quantification.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660
As for a version of the parcellation with network assignments, see here:
https://github.com/ColeLab/ColeAnticevicNetPartition
cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of
As an aside, the S1200 Group Average dataset available at
https://db.humanconnectome.org/data/projects/HCP_1200 includes a version of the
Gordon parcellation with the parcels reordered according to networks, which is
very useful when viewing matrices for network-related structure. Based on
Hi,
You cannot create a z-stat map from a beta map. We suggest that you use PALM
to compute group-wise statistics from individual subject beta (cope) maps.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Email: mha...@wustl.edu
From: "Glasser, Matthew"
Date: Tuesday, February 26, 2019 at 8:19 PM
To: NEUROSCIENCE tim , Leonardo Tozzi
Cc: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] ICA FIX output missing
Regarding task analysis,
.edu
From: "Glasser, Matthew"
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi , "Harms, Michael" ,
"hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] ICA FIX output missing
You’ll want to be using wb_command 1.3.2. I am not aware of any modificatio
Hi,
The log files for ICA FIX are a bit scattered.
In the .ica directory check: .fix_2b_predict.log (from the prediction – i.e,. R
code) and .fix.log (from the cleaning stage).
And in the .ica/fix directory, check logMatlab.txt (I believe that is from the
feature extraction stage).
Note that
South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Anita Sinha
Date: Wednesday, February 20, 2019 at 9:25 AM
To: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users]
See this paper:
https://www.ncbi.nlm.nih.gov/pubmed/30291974
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Another way to put this is that hippocampus is not cortical (it is part of the
medial wall), and thus FreeSurfer does not attempt to generate surfaces that
follow the structures in that region. They even have a FAQ on that specific
question:
Hi,
We’d suggest that you use PALM for inference.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Hi,
We are working on getting the link functioning.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel:
Supporting “arbitrary” formats requires putting a whole system in place for
describing the format, and making it queryable. The good thing is that if the
pconn’s are available, users could use those inputs to their own derived
graph-theoretic measures.
Cheers,
-MH
--
Michael Harms, Ph.D.
Re 1)
If you are using a modern version of ‘dcm2niix’, then in the context of the T1
and T2 scans, the values for T1wSampleSpacing and T2wSampleSpacing are
available as the “DwellTime” entry in the BIDS-style json sidecar files.
Cheers,
-MH
--
Michael Harms, Ph.D.
2019 at 4:40 PM
To: "Harms, Michael" , "Glasser, Matthew"
, "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into
HCP_2mm MNI Surface and Volume space
Hi we just used the isotropic T1w scan
A. Benjamin Sriva
Hi,
I’m curious, did you run the hippocampal/amygdala segmentation using only a
isotropic T1w scan, or did you add in a high in-plane resolution T2w, as is
often used for best performance of the hp/amyg segmentation routine?
Cheers,
-MH
--
Michael Harms, Ph.D.
nifer"
Date: Tuesday, January 22, 2019 at 9:48 AM
To: Xuhong Liao , hcp-users
, "Harms, Michael"
Subject: Re: [HCP-Users] Detailed manual rating score of structural images
Hi Xuhong,
All of the structural data released by HCP is of good or excellent quality
(scores of 3-4 on ou
Hi,
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=88901591
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Anita Sinha
Date: Thursday, January 17, 2019 at 4:38 PM
To: "Glasser, Matthew" , "Harms, Michael"
, "hcp-users@humanconnectome.org"
Subject: Re: [HCP
Hi,
It sounds like you don’t have the gifti library properly installed.
Within matlab, what happens when you type
g = gifti
Do you get a gifti structure?
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Hi,
Please see comments related to this in Examples/DiffusionPreprocessingBatch.sh.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660
Hi,
tSNR (and a fairly sophisticated variance partitioning) is available via the
“RestingStateStats” pipeline.
If you have the full sets of packages from HCP-YA, see the
${subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_stats.txt file,
which includes a “tSNR” entry.
(Associated
If you are looking for a network assignment of the parcels in the Glasser
parcellation, see:
https://github.com/ColeLab/ColeAnticevicNetPartition
cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington
Hi,
I don’t think that those values in the .fsf file get used for anything in terms
of the HCPpipelines, so in that sense their value is irrelevant. Perhaps Greg
will recall if they were set in any meaningful manner way-back when we
constructed the design.fsf templates.
Cheers,
-MH
--
of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: "Glasser, Matthew"
Date: Thursday, December 13, 2018 at 2:02 PM
To: Shachar Gal
Cc: "Harms, Michae
ciftisavereset wasn’t compiled in to the existing 1.067 compiled matlab. I
just tested a new compiled in which this is fixed. Waiting for Oxford to
either update the fix1.067 package, or release a new fix version.
Cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
It’s the standard FreeSurfer label table --
$FREESURFER_HOME/FreeSurferColorLUT.txt
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
Hi,
The error in palm_miscread.m is telling you that your execution environment
isn’t finding ‘wb_command’ in your PATH, so you need to resolve that by setting
up your environment appropriately.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Hi,
The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the
FIX distribution, which is called by the fix script itself.
The only relevant aspect of hcp_fix to that process is that hcp_fix creates the
following symbolic link:
if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ;
Hi,
What is the overall context of this inquiry? Are you getting errors with
running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to
using the version of hcp_fix supplied with the FIX distribution itself. That
doesn’t include some of the enhancements that Matt mentioned
-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Reza Rajimehr
Date: Friday, November 16, 2018 at 1:50 PM
To: "Harms, Michael"
Cc: "Glasser, Matthew" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Number of cortical ver
No, it is more complicated than that.
I believe what you need is -cifti-export-dense-mapping
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box
Hi,
1) We didn’t repeat the exercise of generating an “unrelated subjects” list
following the complete S1200, and rather doubt that we will at this point in
time. Sorry.
2) There is no unique “unrelated subjects” list, since you can pick any one
participant from each family. We generated
Hi,
Have you configured your R installation correctly, per the FSL FIX Wiki page?
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide
cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School
.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: "Harms, Michael&q
FS: 5.3.0-HCP. We are working toward compatibility with FS 6.x – hopefully in
the not too distant future.
FSL: latest (5.0.11 currently)
Workbench: latest (1.3.2 currently)
We know that the following is way out of date, and needs to be updated:
As an aside, if ‘ft_read_cifti’ is expanding all the data to type double (64
bit), then you are looking at needing > 66 GB to load a 91282x91282 dconn.nii
in matlab. I assume that is what is happening based on your experience.
If you want to see how far you can get in Matlab, I would at least
Hi,
See http://www.ncbi.nlm.nih.gov/pubmed/23668970
specifically Figure 9.
“dc” is the readout distortion correction.
“restore” is the bias field correction (for the receive bias field)
The gradient distortion correction is not included as part of the filename, so
the file could just as well
Hi,
You can find that info in the "3T/7T MRI Session Summary CSVs" available for
download via
https://db.humanconnectome.org/data/projects/HCP_1200
cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington
st because of
data footprint issue on compute clusters).
Are those files available via CREST?
Thank you!
nicola
On 09/25/2018 03:17 PM, Harms, Michael wrote:
> Hi,
> You can obtain the entire FreeSurfer output via the Structural Extended
> packages. Perhaps that would be an easier way
Hi,
You can obtain the entire FreeSurfer output via the Structural Extended
packages. Perhaps that would be an easier way for you to proceed?
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington
1. The translations are in mm. I don’t recall off the top of head whether the
rotations are in degrees or rotations, but I believe that is documented in the
release manual. (Or check the HCP Pipeline code).
2. RMS is based on a combination of both the translations and rotations.
3. Yes.
Hi,
You can use -cifti-parcellate with, e.g., the Glasser parcellation.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid
Hi,
As the link to the FS page that Jenn provided makes clear, the FS value for
“ICV” is solely an estimate derived from the determinant of the talairach
transform. You cannot actually measure a true ICV using just a T1w image.
Also, be aware that we didn’t QC the accuracy of the talairach
Hi,
Script to generate scenes for structural QC are available here:
https://github.com/Washington-University/StructuralQC
The joint lecture/practical on “Data Quality” for the HCP course, available
here for the 2017 Course, would be useful for you to review as well:
FWIW, the readout distortion effect in the structurals is such a small effect
that it is difficult to confirm the appropriate polarities for that correction
by trial and error.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor
Hi,
Note that UnwarpDir in the PreFreeSurfer script is a very different thing from
UnwarpDir in the fMRIVolume script. In the former, it specifies the *readout*
direction of the *structurals* -- typically ‘z’ for how we collect T1 and T2
structurals on Siemens scanners (assuming that the
Hi,
FSL/FEAT are not currently equipped to handle grayordinate data.
We have examples of a “third-level” (across subject) analyses as part of the
Practicals in the HCP Course. The content for the 2018 course (in June) will
hopefully become available online in the near future. Until then, the
Hi,
Sorry, but not to my knowledge. We use ‘dcm2niix’ currently for DICOM to NIFTI
conversion (‘dcm2niix’ generates nice .json files containing a bunch of
relevant parameters of the scan). That particular step is pretty
straightforward.
Then, as part of our “session building” process, we
Via Essa Yacoub:
from Stam's paper -
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720790/
Sampling in q-space includes 3 shells at b=1000, 2000 and 3000 s/mm2 (diffusion
times are Δ=43.1 ms and d=10.6 ms, and Gmax=97.4 mT/m after vendor supplied
gradient duty cycle optimization).
--
of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Darko Komnenić
Date: Wednesday, August 8, 2018 at 2:08 PM
To: "Glasser, Matthew"
Cc: "Harms, Michael" , "Winkle
(NIH/NIMH) [E]"
Date: Tuesday, August 7, 2018 at 3:02 PM
To: Darko Komnenić , "Harms, Michael"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Finding a significant difference only in one hemisphere
Hi Darko,
The option “-saveglm” in PALM should produce
Yes, if you have 4 runs in your level 2, then you probably need to start with
fresh templates derived from a 4 run volume analysis.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of
Are you looking in $SUBJID/MNINonLinear/Results/$fMRIName ?
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Hi,
I took a very quick look to see what direction this is heading.
One initlal thing I noticed -- the files in $SUBJID/T1w are not in MNI152 space.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington
of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Marc Dubin
Date: Saturday, July 21, 2018 at 11:13 PM
To: "Harms, Michael"
Cc: "Glasser, Matthew" , "hcp-users@human
University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Marc Dubin
Date: Saturday, July 21, 2018 at 10:28 PM
To: "Harms, Michael"
Cc: "G
, July 19, 2018 at 9:46 PM
To: "Glasser, Matthew"
Cc: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh
input
I used the Matlab DICOM viewer and got BWPPPE as a private f
Dubin
Cc: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Generating Field Maps for
PreFreeSurferPipelineBatch.sh input
I would just pull the numbers directly from the indicated DICOM fields using a
DICOM header viewer such as this one:
ht
,
Another quick question…
What would be appropriate values for:
DwellTime
SEUnwarpDir
TopupConfig
Thanks!
Marc
On 18 Jul 2018, at 0:20, Harms, Michael wrote:
> Hi,
> If you are using SEFMs, you don't need to generate magnitude and phase
> field maps. It is handled internally. S
Hi,
If you are using SEFMs, you don't need to generate magnitude and phase field
maps. It is handled internally. See the Batch script in the Examples
directory.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of
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